RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780714|ref|YP_003065127.1| tRNA (guanine-N(1)-)-methyltransferase [Candidatus Liberibacter asiaticus str. psy62] (236 letters) >gnl|CDD|30684 COG0336, TrmD, tRNA-(guanine-N1)-methyltransferase [Translation, ribosomal structure and biogenesis]. Length = 240 Score = 323 bits (830), Expect = 2e-89 Identities = 117/229 (51%), Positives = 166/229 (72%), Gaps = 4/229 (1%) Query: 3 FHASILTLYPEMFPGHLEKSVAGKALACNLWSMDAIQIRNFSTDRHHSVDDTPAGGGAGM 62 ILTL+PEMF G+L S+ G+A+ L S++ + R+F+TD+H +VDDTP GGGAGM Sbjct: 1 MKIDILTLFPEMFDGYLGYSILGRAIEKGLLSLEVVNPRDFATDKHKTVDDTPYGGGAGM 60 Query: 63 VLRVDILGKAIDHAVSQYTHEDIPRILMSPRGKTLTQKRVRQLSQKLGVIIVCGRFEGID 122 V++ + L A+D + IL+SP+GK TQ R R+L+++ ++++CGR+EGID Sbjct: 61 VMKPEPLFDALDSVKAAKKA---KVILLSPQGKPFTQARARELAKEEHLVLICGRYEGID 117 Query: 123 ERIIEARDLEEISVGDYILSGGEPAALILLDAVVRLLPGVLGNQQSTIHESFE-NGLLEF 181 ER+IE EEIS+GDY+L+GGE AA++L+DAVVRL+PGVLGN++S +SFE NGLLE+ Sbjct: 118 ERVIELYVDEEISIGDYVLTGGELAAMVLIDAVVRLIPGVLGNEESLEEDSFENNGLLEY 177 Query: 182 PQYTRPQIWEGLAIPPILNSGDHERIKKWRKEQSFALTKKHRPDLLSKK 230 P YTRP+ +EG+ +P +L SG+H +I +WR EQS TK+ RPDLL Sbjct: 178 PHYTRPREFEGMKVPEVLLSGNHAKIAQWRLEQSLERTKERRPDLLEAH 226 >gnl|CDD|110724 pfam01746, tRNA_m1G_MT, tRNA (Guanine-1)-methyltransferase. This is a family of tRNA (Guanine-1)-methyltransferases EC:2.1.1.31. In E.coli K12 this enzyme catalyses the conversion of a guanosine residue to N1-methylguanine in position 37, next to the anticodon, in tRNA. Length = 185 Score = 137 bits (346), Expect = 3e-33 Identities = 68/184 (36%), Positives = 102/184 (55%), Gaps = 16/184 (8%) Query: 41 RNFSTDRHHSVDDTPAGGGAGMVLRVDILGKAIDHAVSQYTHEDIPRILMSPRGKTLTQK 100 R+++ +R +VDD GGG GMVL+ + +A+ +VS + IL++P G +Q+ Sbjct: 18 RDYTANRRATVDDHLYGGGFGMVLKPEPDLEAL-KSVSGWEV-----ILLTPTGIPFSQE 71 Query: 101 RVRQLSQKLGVIIVCGRFEGIDERIIEARDLEEISVGDYILSGGEPAALILLDAVVRLLP 160 +L +K ++ + G +EG+ ER+ + D E +G + GGE AL L+DAVV LLP Sbjct: 72 LASELFKKEHLVYLTGDYEGVLERLDD--DKAEYIIGGIVDKGGEKGALTLIDAVVALLP 129 Query: 161 GVLGNQQSTIHESFENGLLEFPQYTRPQIWEGLAIPPILNSGDHERIKKWRKEQSFALTK 220 GVL N S +SF LL P YTRP +P IL SG+H +I+ W E++ T Sbjct: 130 GVL-NTASLPLDSF---LLGVPNYTRPLTLN--QVPEILLSGNHAKIRNW--EEALLRTI 181 Query: 221 KHRP 224 R Sbjct: 182 PKRK 185 >gnl|CDD|32804 COG2985, COG2985, Predicted permease [General function prediction only]. Length = 544 Score = 31.4 bits (71), Expect = 0.19 Identities = 21/95 (22%), Positives = 33/95 (34%), Gaps = 2/95 (2%) Query: 63 VLRVDILGKAIDHAVS-QYTHEDIPRILMSPRGKTLTQKRVRQLSQKLGVIIVCGRFEGI 121 + +V++ +A A +P I L +R L + C R + Sbjct: 179 LFKVNLDTEAQQIARERGLDTVYLPVIRAYVVNPNLDGLNLRDLPILRQEGVYCSRIKRD 238 Query: 122 DERIIEARDLEEISVGDYILSGGEPAALILLDAVV 156 + D I VGD + G P AL LD + Sbjct: 239 GILAVPDPD-TIIQVGDELHLVGYPDALARLDLRI 272 >gnl|CDD|144620 pfam01094, ANF_receptor, Receptor family ligand binding region. This family includes extracellular ligand binding domains of a wide range of receptors. This family also includes the bacterial amino acid binding proteins of known structure. Length = 344 Score = 30.5 bits (69), Expect = 0.40 Identities = 23/87 (26%), Positives = 39/87 (44%), Gaps = 7/87 (8%) Query: 100 KRVRQLSQKLGVIIVCGRFEGIDERIIEARDLEEISVGDYILSGGEPAALILLDAVVRLL 159 K ++ + K VI+VCG + + + + +AR+L +S G Y+ + LL + Sbjct: 169 KELKDIKSKARVIVVCGSSDDLRQILQQARELGMMS-GGYVWILTDLWGDSLLPDNDKAR 227 Query: 160 P---GVLGNQQSTIHESFENGLLEFPQ 183 GVLG T+ G EF + Sbjct: 228 EAAKGVLG---FTLKPPDSPGFQEFLE 251 >gnl|CDD|145056 pfam01702, TGT, Queuine tRNA-ribosyltransferase. This is a family of queuine tRNA-ribosyltransferases EC:2.4.2.29, also known as tRNA-guanine transglycosylase and guanine insertion enzyme. Queuine tRNA-ribosyltransferase modifies tRNAs for asparagine, aspartic acid, histidine and tyrosine with queuine. It catalyses the exchange of guanine-34 at the wobble position with 7-aminomethyl-7-deazaguanine, and the addition of a cyclopentenediol moiety to 7-aminomethyl-7-deazaguanine-34 tRNA; giving a hypermodified base queuine in the wobble position. The aligned region contains a zinc binding motif C-x-C-x2-C-x29-H, and important tRNA and 7-aminomethyl-7deazaguanine binding residues. Length = 238 Score = 28.8 bits (65), Expect = 1.4 Identities = 21/59 (35%), Positives = 28/59 (47%), Gaps = 7/59 (11%) Query: 107 QKLGVIIVCGRFEGIDERIIEARDLEEISVGDYILSG---GEPAALI--LLDAVVRLLP 160 Q L I+ G +E D R A +L E+ Y + G GE + L+DAV LLP Sbjct: 55 QALFGIVQGGLYE--DLREESAEELAELDFDGYAIGGLSVGEEKEEMLELVDAVTPLLP 111 >gnl|CDD|38283 KOG3073, KOG3073, KOG3073, Protein required for 18S rRNA maturation and 40S ribosome biogenesis [Translation, ribosomal structure and biogenesis]. Length = 236 Score = 28.0 bits (62), Expect = 2.0 Identities = 18/78 (23%), Positives = 34/78 (43%), Gaps = 8/78 (10%) Query: 69 LGKAIDHAVSQYTHEDIPRILMSPRGKTLT--QKRVRQLSQKLGVIIVCGRF--EGIDER 124 L K + + V+ + + +I +S G L+ + V L V+ V G I Sbjct: 144 LLKVVKNPVTDHLPVNSRKIGLSFSGPKLSNVRDLVASLDDDDSVVFVIGAMAHGKISVE 203 Query: 125 IIEARDLEEISVGDYILS 142 ++ E++S+ +Y LS Sbjct: 204 YVD----EKVSISNYPLS 217 >gnl|CDD|146300 pfam03587, EMG1, EMG1/NEP1 methyltransferase. Members of this family are essential for 40S ribosomal biogenesis. The structure of EMG1 has revealed that it is a novel member of the superfamily of alpha/beta knot fold methyltransferases. Length = 202 Score = 28.3 bits (64), Expect = 2.1 Identities = 17/76 (22%), Positives = 34/76 (44%), Gaps = 2/76 (2%) Query: 69 LGKAIDHAVSQYTHEDIPRILMSPRGKTLTQKRVRQLSQKLGVIIVCGRF--EGIDERII 126 L K + + ++ E +IL+S +G+ ++ K + + V V G F + + Sbjct: 114 LLKVVKNPLTDLLPEGSKKILLSEKGEKVSPKELASELKNEPVAFVIGAFPHGDFSDEVD 173 Query: 127 EARDLEEISVGDYILS 142 + E S+ +Y LS Sbjct: 174 YKKADESYSISNYPLS 189 >gnl|CDD|31942 COG1756, Mra1, Uncharacterized conserved protein [Function unknown]. Length = 223 Score = 27.9 bits (62), Expect = 2.2 Identities = 16/55 (29%), Positives = 25/55 (45%), Gaps = 1/55 (1%) Query: 88 ILMSPRGKTLTQKRVRQLSQKLGVIIVCGRFEGIDERIIEARDLEEISVGDYILS 142 IL+ +G+ + K + L K +I+ G G D R E+ S+ D LS Sbjct: 151 ILLHEKGELIPPKELISLLLKGIAVIIGGFPHG-DFREETEFVAEKYSIYDEPLS 204 >gnl|CDD|176347 cd01271, Fe65_C, Fe65 C-terminal Phosphotyrosine-binding (PTB) domain. Fe65 C-terminal Phosphotyrosine-binding (PTB) domain. Fe65 is an amyloid beta A4 precursor (APP) protein-binding. It contains an N-terminal WW domain followed by two PTB domains. The C-terminal PTB domain is responsible for APP binding. PTB domains have a PH-like fold and are found in various eukaryotic signaling molecules. They were initially identified based upon their ability to recognize phosphorylated tyrosine residues In contrast to SH2 domains, which recognize phosphotyrosine and adjacent carboxy-terminal residues, PTB-domain binding specificity is conferred by residues amino-terminal to the phosphotyrosine. More recent studies have found that some types of PTB domains can bind to peptides which are not tyrosine phosphorylated or lack tyrosine residues altogether. Length = 124 Score = 26.8 bits (59), Expect = 6.2 Identities = 20/72 (27%), Positives = 26/72 (36%), Gaps = 16/72 (22%) Query: 47 RHHSVDDTPAGGGAGMVLRVDILGKAIDHAVSQYTHED------------IPRILMSPRG 94 R + P GM +IL AID+ +S ED I I Sbjct: 5 RVQYLGMLPVDKPTGM----EILNSAIDNLMSSSNKEDWLSVNVNVAPSTITVISEKNEE 60 Query: 95 KTLTQKRVRQLS 106 + L + RVR LS Sbjct: 61 EVLVECRVRYLS 72 >gnl|CDD|30836 COG0490, COG0490, Putative regulatory, ligand-binding protein related to C-terminal domains of K+ channels [Inorganic ion transport and metabolism]. Length = 162 Score = 26.4 bits (58), Expect = 6.4 Identities = 12/51 (23%), Positives = 21/51 (41%), Gaps = 1/51 (1%) Query: 96 TLTQKRVRQLSQKLGVIIVCGRFEGIDERIIEARDLEEISVGDYILSGGEP 146 +LT + RQ++ LG+ RFE E + +E + G+ Sbjct: 53 SLTDEEARQVAAILGMSYKTERFEQT-EPALPGLIIEWFKIEAGSPFIGKT 102 >gnl|CDD|144312 pfam00665, rve, Integrase core domain. Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. The amino-terminal domain is a zinc binding domain pfam02022. This domain is the central catalytic domain. The carboxyl terminal domain that is a non-specific DNA binding domain pfam00552. The catalytic domain acts as an endonuclease when two nucleotides are removed from the 3' ends of the blunt-ended viral DNA made by reverse transcription. This domain also catalyses the DNA strand transfer reaction of the 3' ends of the viral DNA to the 5' ends of the integration site. Length = 120 Score = 26.1 bits (58), Expect = 8.8 Identities = 21/98 (21%), Positives = 35/98 (35%), Gaps = 18/98 (18%) Query: 32 LWSMDAIQIRNFSTDR----HHSVDDTPAGGGAGMVL--------RVDILGKAIDHAVSQ 79 LW MD I S VDD + V+ +++ + AV + Sbjct: 8 LWQMDITGIPIPSKGGKKYLLVIVDDF-----SRFVVAYALKSKTDAELVFDLLKAAVER 62 Query: 80 YTHEDIPRILMSPRGKTLTQKRVRQLSQKLGVIIVCGR 117 P+ + S G T K ++L ++LG+ R Sbjct: 63 R-GGKKPKTIHSDNGSEFTSKAFQELLKELGIKHSFSR 99 >gnl|CDD|144614 pfam01086, Clathrin_lg_ch, Clathrin light chain. Length = 225 Score = 25.8 bits (57), Expect = 9.6 Identities = 7/35 (20%), Positives = 17/35 (48%), Gaps = 3/35 (8%) Query: 196 PPILNSGDHERIKKWRKEQSFALTKKHRPDLLSKK 230 + + E I++WR+ + + ++ D S+K Sbjct: 103 ADRVEGEEPESIREWRERRDLRIEER---DEASEK 134 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 0.320 0.138 0.408 Gapped Lambda K H 0.267 0.0798 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 2,941,232 Number of extensions: 156094 Number of successful extensions: 393 Number of sequences better than 10.0: 1 Number of HSP's gapped: 386 Number of HSP's successfully gapped: 16 Length of query: 236 Length of database: 6,263,737 Length adjustment: 91 Effective length of query: 145 Effective length of database: 4,297,318 Effective search space: 623111110 Effective search space used: 623111110 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: 56 (25.2 bits)