RPS-BLAST 2.2.22 [Sep-27-2009]
Database: mmdb70
33,805 sequences; 4,956,049 total letters
Searching..................................................done
Query= gi|254780904|ref|YP_003065317.1| tRNA/rRNA methyltransferase
[Candidatus Liberibacter asiaticus str. psy62]
(268 letters)
>3kty_A Probable methyltransferase; alpha-beta-alpha sandwich,
structural genomics, PSI-2, protein structure
initiative; 2.30A {Bordetella pertussis} (A:)
Length = 173
Score = 98.4 bits (244), Expect = 8e-22
Identities = 50/168 (29%), Positives = 75/168 (44%), Gaps = 6/168 (3%)
Query: 7 QLQNSAKGPVIILVDPQLGENIGMVARAMWNFNLTQLRLVNPRDGW--PSEKARSSSANA 64
+ I P N+G ARA+ +L LV PR +A + ++ A
Sbjct: 3 AXTQAFSRVRFIXTQPSHPGNVGSAARAIKTXGFGELVLVAPRFPDXTAQPEAVALASGA 62
Query: 65 DCVIDSVRVFSNLKEAIADLHFIYATTARNRNNFKSVLAPKE---AAIVLNERIFSGQNV 121
V++ V L+EA+A + +A T R R+ +E A + +G V
Sbjct: 63 LDVLERAAVHDTLEEALAPVTLAFALTTRVRDLGPPPCDIREAAGLARRHLDDTEAG-VV 121
Query: 122 GIIFGRERWGLTNEEIALSNAIISFPVNPLFPSLNISQAVLLMVWECM 169
I+ G ER GLTN +I L + I P NP + SLN++QA+ L WE
Sbjct: 122 AIVLGTERAGLTNAQIELCHRICHIPANPQYSSLNVAQALQLAAWELR 169
>3dcm_X AdoMet, uncharacterized protein TM_1570; trefoil knot, spout
mtase, adoMet binding, transferase; HET: SAM; 2.00A
{Thermotoga maritima} (X:)
Length = 192
Score = 93.4 bits (231), Expect = 3e-20
Identities = 20/166 (12%), Positives = 50/166 (30%), Gaps = 12/166 (7%)
Query: 14 GPVIILVDPQLGENIGMVARAMWNFNLTQLRLVNPRDGWP-----------SEKARSSSA 62
I+ ++ +AR +NL +V +
Sbjct: 17 KDGSIISTAVTNLDVHDIARTARTYNLKGYYIVTNLRAQQDMVSKMLKFWREGFGSRYNP 76
Query: 63 NADCVIDSVRVFSNLKEAIADLHFIYATTARNRNNFKSVLAPKEAAIVLNERIFSGQNVG 122
+ + V++ S L++ + D+ + + I +
Sbjct: 77 SRAESLKLVKLKSYLEDVLEDIESVEGERPLIFFTSAKKRENDISFEEGRRIIIETEKPV 136
Query: 123 IIFGRERWGLTNEEIALSNAIISF-PVNPLFPSLNISQAVLLMVWE 167
+I WGL +E + +S+ ++ F L++ A +++
Sbjct: 137 LILLGTGWGLPDEILEISDYVLEPIRAQSDFNHLSVRAAAAIIIDR 182
>3ilk_A Uncharacterized tRNA/RRNA methyltransferase HI0380;
APC63004, methylase family protein, haemophilus
influenzae RD KW20; 2.01A {Haemophilus influenzae}
(A:1-174)
Length = 174
Score = 91.0 bits (225), Expect = 2e-19
Identities = 53/157 (33%), Positives = 88/157 (56%), Gaps = 5/157 (3%)
Query: 13 KGPVIILVDPQLGENIGMVARAMWNFNLTQLRLVNPRDGWPSEKARSSSANADCVIDSVR 72
+ I+L++ NIG ARA LTQL LV+P+ E++ + SA A+ ++ + R
Sbjct: 6 ENIRIVLIETSHSGNIGSAARAXKTXGLTQLCLVSPK--SVDEQSYALSAGAENIVKNAR 63
Query: 73 VFSNLKEAIADLHFIYATTARNRNNFKSVLAPKEAAIVLNERIFSGQNVGIIFGRERWGL 132
V + EA+ D + T+AR R+ +++ P+E A + + + I+FGRER GL
Sbjct: 64 VVDSFDEAVDDCSLVIGTSARLRHLQNTLIEPRECAE---KVVAYKGKIAIVFGRERIGL 120
Query: 133 TNEEIALSNAIISFPVNPLFPSLNISQAVLLMVWECM 169
TNEE+ + ++ P NP + SLN++ AV L+ +E
Sbjct: 121 TNEELLKCHYHLNIPANPDYSSLNLAXAVQLVSYELR 157
>3ic6_A Putative methylase family protein; structural genomics,
PSI-2, protein structure initiative, midwest center for
structural genomics; 2.59A {Neisseria gonorrhoeae fa
1090} (A:1-201)
Length = 201
Score = 89.2 bits (220), Expect = 5e-19
Identities = 48/183 (26%), Positives = 79/183 (43%), Gaps = 19/183 (10%)
Query: 6 PQLQNSAKGPVIILVDPQLGENIGMVARAMWNFNLTQLRLVNPRDGWP------------ 53
P L + IIL NIG ARA L +L +V P
Sbjct: 9 PALPDYLGNIRIILTRTSHPANIGSAARAXKTXGLHRLTIVTPNLXATPXTENPPVFNPD 68
Query: 54 -------SEKARSSSANADCVIDSVRVFSNLKEAIADLHFIYATTARNRNNFKSVLAPKE 106
E++ ++ A V+ + + + L EA+AD A T+R R + P++
Sbjct: 69 DVQSFALPEESFILASGAADVLHNAEIVATLDEALADTTIACALTSRRREITAPLQTPRD 128
Query: 107 AAIVLNERIFSGQNVGIIFGRERWGLTNEEIALSNAIISFPVNPLFPSLNISQAVLLMVW 166
L + G+ V ++FG E +GL+ EE+ N + + NP + SLN++QAV ++ +
Sbjct: 129 LVPELLQAANRGEKVALVFGNETFGLSIEEVRACNRLXTINGNPDYFSLNLAQAVQVVCY 188
Query: 167 ECM 169
E
Sbjct: 189 EIF 191
>1x7o_A Avirb, rRNA methyltransferase; SPOU, C-terminal knot, seMet;
2.37A {Streptomyces viridochromogenes} PDB: 1x7p_A*
(A:119-287)
Length = 169
Score = 86.9 bits (214), Expect = 3e-18
Identities = 26/163 (15%), Positives = 50/163 (30%), Gaps = 6/163 (3%)
Query: 7 QLQNSAKGPVIILVDPQLGENIGMVARAMWNFNLTQLRLVNPRDGWPSEKARSSSANADC 66
++ ++ P NIG + R+ L + K+ SS +
Sbjct: 1 RIPVREDFLGVLFDRPTSPGNIGSIIRSADALGAHGLIVAGHAADVYDPKSVRSSTGSLF 60
Query: 67 VIDSVRVFSNLKEAIADLHFIYATTARNRNNFKSVLAPKEAAIVLNERIFSGQNVGIIFG 126
+ + E + R ++ E Q ++ G
Sbjct: 61 SLP-AVRVPSPGEVXDWVE-----ARRAAGTPIVLVGTDEHGDCDVFDFDFTQPTLLLIG 114
Query: 127 RERWGLTNEEIALSNAIISFPVNPLFPSLNISQAVLLMVWECM 169
E GL+N L + +S P SLN + A +++E +
Sbjct: 115 NETAGLSNAWRTLCDYTVSIPXAGSASSLNAANAATAILYEAV 157
>2i6d_A RNA methyltransferase, TRMH family; stuctural genomics,
knot, structural genomics, PSI-2, protein structure
initiative; HET: MSE; 1.85A {Porphyromonas gingivalis
W83} (A:99-257)
Length = 159
Score = 86.5 bits (213), Expect = 3e-18
Identities = 25/169 (14%), Positives = 51/169 (30%), Gaps = 18/169 (10%)
Query: 6 PQLQNSAKGPVIILVDPQLGENIGMVARAMWNFNLTQLRLVNPRDGWPSEKARSSSANAD 65
P ++ ++L Q N+G + R F + + L S K +S A
Sbjct: 1 PVVEG----LTLLLDGVQDPGNVGTILRTADWFGIRHVWLGTGSADVFSPKVVQASXGAL 56
Query: 66 CVIDSVRVFSNLKEAIADLHFIYATTARNRNNFKSVLAPKEAAIVLNERIFSGQNVGIIF 125
+ + R + ++ + ++
Sbjct: 57 ARVQPTPL---------KNTVDTLAYFRRQGIPVYGAFLDGQSLYEAPLPNFTEPAILVL 107
Query: 126 GRERWGLTNEEIALSNAIISFPVNPLFP-----SLNISQAVLLMVWECM 169
G E G++ E A ++ P + L SLN++ A ++ E
Sbjct: 108 GSEGRGISPEVAAEITDRLTIPASGLSVKGHTESLNVAIATAILCSEWR 156
>1v2x_A TRNA (GM18) methyltransferase; DEEP trefoil knot, riken
structural genomics/proteomics initiative, RSGI,
structural genomics; HET: SAM; 1.50A {Thermus
thermophilus} (A:21-176)
Length = 156
Score = 83.8 bits (206), Expect = 2e-17
Identities = 28/154 (18%), Positives = 59/154 (38%), Gaps = 12/154 (7%)
Query: 16 VIILVDPQLGENIGMVARAMWNFNLTQLRLVNPRDGWPSEKARSSSANADCVIDSVRVFS 75
++L + N+ + R + + VNP G P+ S ++ +
Sbjct: 4 TVLLENVHKPHNLSAILRTCDAVGVLEAHAVNPTGGVPTFNETSGGSHKWVYLRVHPDLH 63
Query: 76 NLKEAIADLHFIYATTARNRNNFKSVLAPKEAAIVLNERIFSGQNVGIIFGRERWGLTNE 135
+ + F TA + + + ++FG E+WG++ E
Sbjct: 64 EAFRFLKERGFTVYATALREDARDF------------REVDYTKPTAVLFGAEKWGVSEE 111
Query: 136 EIALSNAIISFPVNPLFPSLNISQAVLLMVWECM 169
+AL++ I P+ + SLN+S A ++++E
Sbjct: 112 ALALADGAIKIPMLGMVQSLNVSVAAAVILFEAQ 145
>1gz0_A Hypothetical tRNA/RRNA methyltransferase YJFH;
2'O-methyltransferase, knot, montreal- kingston
bacterial structural genomics initiative, BSGI; 2.5A
{Escherichia coli} (A:90-253)
Length = 164
Score = 83.3 bits (205), Expect = 3e-17
Identities = 24/162 (14%), Positives = 55/162 (33%), Gaps = 11/162 (6%)
Query: 8 LQNSAKGPVIILVDPQLGENIGMVARAMWNFNLTQLRLVNPRDGWPSEKARSSSANADCV 67
+ + + ++IL N+G R+ + + + R + A+ + A
Sbjct: 10 IASLDQPFLLILDGVTDPHNLGACLRSADAAGVHAVIVPKDRSAQLNATAKKVACGAAES 69
Query: 68 IDSVRVFSNLKEAIADLHFIYATTARNRNNFKSVLAPKEAAIVLNERIFSGQNVGIIFGR 127
+ +RV + + T + ++ A + + ++ G
Sbjct: 70 VPLIRVTN-----------LARTXRXLQEENIWIVGTAGEADHTLYQSKXTGRLALVXGA 118
Query: 128 ERWGLTNEEIALSNAIISFPVNPLFPSLNISQAVLLMVWECM 169
E G + +IS P SLN+S A + ++E +
Sbjct: 119 EGEGXRRLTREHCDELISIPXAGSVSSLNVSVATGICLFEAV 160
>3gyq_A RRNA (adenosine-2'-O-)-methyltransferase; rRNA
methyltransferase, spout mtases, SAM, trefoil knot,
antibiotic resistance; HET: SAM; 2.45A {Streptomyces
cyaneus} (A:113-272)
Length = 160
Score = 83.0 bits (204), Expect = 4e-17
Identities = 26/155 (16%), Positives = 61/155 (39%), Gaps = 10/155 (6%)
Query: 13 KGPVIILVDPQLGENIGMVARAMWNFNLTQLRLVNPRDGWPSEKARSSSANADCVIDSVR 72
+G V++L ++ NIG + R + + LV+ +++ ++ V
Sbjct: 6 RGDVVVLDGVKIVGNIGAIVRTSLALGASGIILVDSDITSIADRRLQRASRGYVFSLPVV 65
Query: 73 VFSNLKEAIADLHFIYATTARNRNNFKSVLAPKEAAIVLNERIFSGQNVGIIFGRERWGL 132
+ A + + + + I + E + + ++FG E+ G
Sbjct: 66 LSGRE----------EAIAFIRDSGMQLMTLKADGDISVKELGDNPDRLALLFGSEKGGP 115
Query: 133 TNEEIALSNAIISFPVNPLFPSLNISQAVLLMVWE 167
++ S+A +S P+ SLN+S ++ + + E
Sbjct: 116 SDLFEEASSASVSIPMMSQTESLNVSVSLGIALHE 150
>1zjr_A TRNA (guanosine-2'-O-)-methyltransferase; methylase, RNA
modifying enzyme, topological knot; 1.85A {Aquifex
aeolicus} (A:24-180)
Length = 157
Score = 82.6 bits (203), Expect = 4e-17
Identities = 18/157 (11%), Positives = 56/157 (35%), Gaps = 11/157 (7%)
Query: 13 KGPVIILVDPQLGENIGMVARAMWNFNLTQLRLVNPRDGWPSEKARSSSANADCVIDSVR 72
K ++ + + N + R + L + ++ + + + +
Sbjct: 1 KDLIVFADNVKNEHNFSAIVRTCDAVGVLYLYYYHAEG-KKAKINEGITQGSHKWVFIEK 59
Query: 73 VFSNLKEAIADLHFIYATTARNRNNFKSVLAPKEAAIVLNERIFSGQNVGIIFGRERWGL 132
V + +++ + + + A + + + ++ G E G+
Sbjct: 60 VDNPVQKLLEFKNRGFQIVATWLSKESVNFREVDY----------TKPTVLVVGNELQGV 109
Query: 133 TNEEIALSNAIISFPVNPLFPSLNISQAVLLMVWECM 169
+ E + +++ I P+ + SLN+S A ++++E
Sbjct: 110 SPEIVEIADKKIVIPMYGMAQSLNVSVATGIILYEAQ 146
>1ipa_A RRMH, RNA 2'-O-ribose methyltransferase; DEEP trefoil knot,
rossmann fold, EL30-like fold, riken structural
genomics/proteomics initiative; 2.40A {Thermus
thermophilus} (A:109-274)
Length = 166
Score = 78.7 bits (193), Expect = 7e-16
Identities = 26/164 (15%), Positives = 54/164 (32%), Gaps = 15/164 (9%)
Query: 7 QLQNSAKGPVIILVDPQLGENIGMVARAMWNFNLTQLRLVNPRDGWPSEKARSSSANADC 66
+ + S +++ V + N+G V R+ + + D + + R+S+
Sbjct: 1 EYRPSPDALILVAVGLEKPGNLGAVLRSADAAGAEAVLVAGGVDLYSPQVIRNSTGVVFS 60
Query: 67 V-IDSVRVFSNLKEAIADLHFIYATTARNRNNFKSVLAPKEAAIVLNERIFSGQNVGIIF 125
+ + L + ATT + AI
Sbjct: 61 LRTLAASESEVLDWIKQHNLPLVATTPHAEALYWEANLRPPVAI--------------AV 106
Query: 126 GRERWGLTNEEIALSNAIISFPVNPLFPSLNISQAVLLMVWECM 169
G E GL + + + P+ SLN+S + L+++E +
Sbjct: 107 GPEHEGLRAAWLEAAQTQVRIPMQGQADSLNVSVSAALLLYEAL 150
>2ha8_A TAR (HIV-1) RNA loop binding protein; methyltransferase,
structural genomics, structural genomics consortium,
SGC, RNA binding protein; HET: SAH; 1.60A {Homo sapiens}
(A:)
Length = 184
Score = 78.4 bits (192), Expect = 9e-16
Identities = 24/162 (14%), Positives = 56/162 (34%), Gaps = 9/162 (5%)
Query: 8 LQNSAKGPVIILVDPQLGENIGMVARAMWNFNLTQLRLVNPRDGWPSEKARSSSANADCV 67
L S +++ N+G + R F + L + + + ++ + S +A+
Sbjct: 20 LGKSISRLIVVASLIDKPTNLGGLCRTCEVFGASVLVVGSLQC-ISDKQFQHLSVSAEQW 78
Query: 68 IDSVRVFSNLKEAIADLHFIYATTARNRNNFKSVLAPKEAAIVLNERIFSGQNVGIIFGR 127
+ V V + + + + A + + + ++ G
Sbjct: 79 LPLVEVKPPQLI--------DYLQQKKTEGYTIIGVEQTAKSLDLTQYCFPEKSLLLLGN 130
Query: 128 ERWGLTNEEIALSNAIISFPVNPLFPSLNISQAVLLMVWECM 169
ER G+ I + + P + SLN+ + L++WE
Sbjct: 131 EREGIPANLIQQLDVCVEIPQQGIIRSLNVHVSGALLIWEYT 172
>1mxi_A YIBK, hypothetical tRNA/RRNA methyltransferase HI0766;
S-adenosylhomocysteine, SPOU family, structure 2
function project; HET: SAH; 1.70A {Haemophilus
influenzae} (A:)
Length = 160
Score = 76.8 bits (188), Expect = 3e-15
Identities = 22/156 (14%), Positives = 47/156 (30%), Gaps = 15/156 (9%)
Query: 16 VIILVDPQLGENIGMVARAMWNFNLTQLRLVNPRDGWPSEKARSSSANADCVIDSVRVFS 75
I+L +P++ +N G + R N + W ++ R S + + R
Sbjct: 3 DIVLYEPEIPQNTGNIIRLCANTGFRLHLIEPLGFTWDDKRLRRSGLDYHEFAEIKRH-K 61
Query: 76 NLKEAIADLHFIYATTARNRNNFKSVLAPKEAAIVLNERIFSGQNVGIIFGRERWGLTNE 135
+ + + + ++FG E G+
Sbjct: 62 TFEAFLESEKPKRLFALTTKGCPAHSQVKFK------------LGDYLMFGPETRGIPMS 109
Query: 136 EIALSNAIISF--PVNPLFPSLNISQAVLLMVWECM 169
+ P+ S+N+S +V + V+E
Sbjct: 110 ILNEMPMEQKIRIPMTANSRSMNLSNSVAVTVYEAW 145
>3e5y_A TRMH family RNA methyltransferase; ssgcid, protein knot,
decode, structural genomics; 2.40A {Burkholderia
pseudomallei 305} (A:)
Length = 160
Score = 74.1 bits (181), Expect = 2e-14
Identities = 27/156 (17%), Positives = 44/156 (28%), Gaps = 13/156 (8%)
Query: 16 VIILVDPQLGENIGMVARAMWNFNLTQLRLVNPRDGWPSEKARSSSANADCVIDSVRVFS 75
++LV+P++ N G V R N + K R + +
Sbjct: 7 NVVLVEPEIPPNTGNVIRLCANTGARLHLIEPLGFPLDDAKMRRAGLDYHEYAQMRVHRD 66
Query: 76 NLKEAIADLHFIYATTARNRNNFKSVLAPKEAAIVLNERIFSGQNVGIIFGRERWGLTNE 135
A A + + A +FG E GL
Sbjct: 67 W-----------DAFVAAEAPDPARMFAFTTRGSGRFHDRAFEPGDWFVFGAETRGLAPA 115
Query: 136 EIALSNAIISF--PVNPLFPSLNISQAVLLMVWECM 169
+ P+ P SLN+S V ++V+E
Sbjct: 116 LVDRFAPEQRVRLPMRPGNRSLNLSNTVAVVVFEAW 151
>3ilk_A Uncharacterized tRNA/RRNA methyltransferase HI0380;
APC63004, methylase family protein, haemophilus
influenzae RD KW20; 2.01A {Haemophilus influenzae}
(A:175-244)
Length = 70
Score = 61.9 bits (151), Expect = 9e-11
Identities = 16/72 (22%), Positives = 32/72 (44%), Gaps = 4/72 (5%)
Query: 186 PATKGELLSFLDYLEISLEERGYFRPVEKKKKMLDDLYSIFIRPELMREEVFLLRGIVST 245
T +L F DY E + G+ + + + L ++ R +L + E+ +L G +S
Sbjct: 3 YPTTDQLAYFFDYTERIYQSLGFIQN----QGVXRKLKRLYYRAKLEKNELNILNGXLSA 58
Query: 246 LDKFSRQSSRRN 257
++K + N
Sbjct: 59 VEKRIDLTKEDN 70
>2k3i_A Uncharacterized protein YIIS; GFT protein structure, PSI,
NESG, structural genomics, protein structure initiative;
NMR {Shigella flexneri 2A} (A:)
Length = 109
Score = 27.1 bits (60), Expect = 2.8
Identities = 15/70 (21%), Positives = 24/70 (34%), Gaps = 8/70 (11%)
Query: 63 NADCVIDSVRVFSNLKEAIADLHFIYATTARNR------NNFKSVLAPKEAAIVLNERI- 115
N +C R F+ +EA + + A + + E + L+
Sbjct: 25 NDNCTSKFSRFFATREEAESFMTK-LKELAAAASSADEGASVAYKIKDLEGQVELDAAFT 83
Query: 116 FSGQNVGIIF 125
FS Q IIF
Sbjct: 84 FSCQAEMIIF 93
>2w3s_B Xanthine dehydrogenase; XO, XDH, GOUT, iron, 2Fe-2S,
iron-sulfur, oxidoreductase, purine metabolism,
molybdenum cofactor, hypoxanthine; HET: MPN FAD XAN;
2.60A {Rhodobacter capsulatus} PDB: 1jrp_B* 2w3r_B*
1jro_B* 2w54_B* 2w55_B* (B:462-606)
Length = 145
Score = 26.0 bits (57), Expect = 4.8
Identities = 7/46 (15%), Positives = 15/46 (32%)
Query: 166 WECMENSIVSSEKNVKEQNTPATKGELLSFLDYLEISLEERGYFRP 211
C ++ V+ E+++ ISL G++
Sbjct: 98 EGCAARDVIFDAGQVQASGKSWRFAEIVAAAYMARISLSATGFYAT 143
Database: mmdb70
Posted date: Jun 20, 2010 3:12 AM
Number of letters in database: 4,956,049
Number of sequences in database: 33,805
Lambda K H
0.318 0.133 0.380
Gapped
Lambda K H
0.267 0.0477 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 33805
Number of Hits to DB: 1,896,878
Number of extensions: 83144
Number of successful extensions: 204
Number of sequences better than 10.0: 1
Number of HSP's gapped: 188
Number of HSP's successfully gapped: 18
Length of query: 268
Length of database: 4,956,049
Length adjustment: 87
Effective length of query: 181
Effective length of database: 2,015,014
Effective search space: 364717534
Effective search space used: 364717534
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: 54 (25.2 bits)