RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy13718
(165 letters)
>3gru_A Dimethyladenosine transferase; rossman fold, ribosomal assem
adenosyl-L-methionine, rRNA, methyltransferase,
RNA-binding processing; HET: AMP; 1.60A
{Methanocaldococcus jannaschii} PDB: 3grr_A* 3grv_A*
3gry_A* 3fyd_A 3fyc_A*
Length = 295
Score = 86.5 bits (215), Expect = 3e-21
Identities = 27/138 (19%), Positives = 52/138 (37%), Gaps = 9/138 (6%)
Query: 1 MIATEGMEQRCRLSIMCQNWCNVDHRFTIPGKAFIPKPQVDVGVVHFTPRVHPIIDLPFK 60
M+A G + RLS+ Q+ +V+ +P AF PKP+V +V P
Sbjct: 154 MVAAAGTKDYGRLSVAVQSRADVEIVAKVPPSAFYPKPKVYSAIVKIKPNKGKYHIENEN 213
Query: 61 LIERVVSCIFRYRQKQVYKPASLLFP---------KRKRQLVVSLLERACVKPILRPYQL 111
+ + IF++R K V K K+ + ++ + ++L
Sbjct: 214 FFDDFLRAIFQHRNKSVRKALIDSSKELNYNKDEMKKILEDFLNTNSEIKNLINEKVFKL 273
Query: 112 SVQEFGQICLAYRDMCEE 129
SV++ + + +
Sbjct: 274 SVKDIVNLSNEFYRFLQN 291
>3ftd_A Dimethyladenosine transferase; KSGA, rossmann-like fold, RNA
methyltransferase, mtase, anti resistance,
methyltransferase, RNA-binding; 1.44A {Aquifex aeolicus}
PDB: 3ftc_A 3fte_A 3ftf_A* 3r9x_B*
Length = 249
Score = 79.1 bits (196), Expect = 9e-19
Identities = 29/118 (24%), Positives = 56/118 (47%), Gaps = 14/118 (11%)
Query: 12 RLSIMCQNWCNVDHRFTIPGKAFIPKPQVDVGVVHFTPR-VHPIIDLPFKLIERVVSCIF 70
LS+ + + +V++ T+P + F+P P+V V+ P+ D K ++ ++ IF
Sbjct: 145 WLSVFVRTFYDVNYVMTVPPRFFVPPPKVQSAVIKLVKNEKFPVKD--LKNYKKFLTKIF 202
Query: 71 RYRQKQVYKPASLLFPKRKRQLVVSLLERACVKPILRPYQLSVQEFGQICLAYRDMCE 128
+ R+K + K + LL+ A + P R QLS+++F ++ D E
Sbjct: 203 QNRRKVLRKK-----------IPEELLKEAGINPDARVEQLSLEDFFKLYRLIEDSGE 249
>3tqs_A Ribosomal RNA small subunit methyltransferase A; protein synthesis;
1.98A {Coxiella burnetii}
Length = 255
Score = 78.3 bits (194), Expect = 2e-18
Identities = 33/109 (30%), Positives = 55/109 (50%), Gaps = 8/109 (7%)
Query: 12 RLSIMCQNWCNVDHRFTIPGKAFIPKPQVDVGVVHFTPRVHPIIDLP-FKLIERVVSCIF 70
RLS+M Q +C+ + FT+ +AF P P+V+ ++ PR + + VV F
Sbjct: 149 RLSVMAQYFCDNTYLFTVSPQAFTPPPRVESAIIRLIPRHNFTPVAKNLDQLSHVVKEAF 208
Query: 71 RYRQKQVYKPASLLFPKRKRQLVVSLLERACVKPILRPYQLSVQEFGQI 119
YR+K V +L K+ + S + P LRP +L+V++F +I
Sbjct: 209 SYRRKTVGN--AL-----KKLINPSQWPLLEINPQLRPQELTVEDFVKI 250
>1qam_A ERMC' methyltransferase; rRNA methyltransferase ERMC', cofactor
analogs; 2.20A {Bacillus subtilis} SCOP: c.66.1.24 PDB:
1qan_A* 1qao_A* 1qaq_A* 2erc_A
Length = 244
Score = 77.6 bits (192), Expect = 3e-18
Identities = 17/123 (13%), Positives = 42/123 (34%), Gaps = 18/123 (14%)
Query: 1 MIATEGMEQRCRLSIMCQNWCNVDHRFTIPGKAFIPKPQVDVGVVHFTPRVHPIIDLPFK 60
++ T+ L++ ++ +P + F PKP+V+ ++ + I +
Sbjct: 135 LLNTKR-----SLALFLMAEVDISILSMVPREYFHPKPKVNSSLIRLNRKKSRISHKDKQ 189
Query: 61 LIERVVSCIFRYRQKQVYKPASLLFPKRKRQLVVSLLERACVKPILRPYQLSVQEFGQIC 120
V K+++ + L+ A I +S ++F +
Sbjct: 190 KYNYFVMKWVNKEYKKIFTKNQFN----------NSLKHA---GIDDLNNISFEQFLSLF 236
Query: 121 LAY 123
+Y
Sbjct: 237 NSY 239
>1qyr_A KSGA, high level kasugamycin resistance protein, S-adenosylMet;
adenosine dimethyltransferase, rRNA modification,
transferase, translation; 2.10A {Escherichia coli} SCOP:
c.66.1.24 PDB: 4adv_V 3tpz_A
Length = 252
Score = 77.2 bits (191), Expect = 5e-18
Identities = 31/109 (28%), Positives = 50/109 (45%), Gaps = 8/109 (7%)
Query: 12 RLSIMCQNWCNVDHRFTIPGKAFIPKPQVDVGVVHFTPRVHPIIDLP-FKLIERVVSCIF 70
RLS+M Q +CNV +P AF P P+VD VV P + +++ R+ + F
Sbjct: 143 RLSVMAQYYCNVIPVLEVPPSAFTPPPKVDSAVVRLVPHATMPHPVKDVRVLSRITTEAF 202
Query: 71 RYRQKQVYKPASLLFPKRKRQLVVSLLERACVKPILRPYQLSVQEFGQI 119
R+K + SL V +L + P +R +SV ++ Q+
Sbjct: 203 NQRRKTIR--NSL-----GNLFSVEVLTGMGIDPAMRAENISVAQYCQM 244
>1i4w_A Mitochondrial replication protein MTF1; mitochondrial transcription
factor, transcription initiation; 2.60A {Saccharomyces
cerevisiae} SCOP: c.66.1.24
Length = 353
Score = 77.3 bits (190), Expect = 1e-17
Identities = 14/145 (9%), Positives = 35/145 (24%), Gaps = 26/145 (17%)
Query: 1 MIATEGMEQRCRLSIMCQNWCNV---------------------DHRFTIPGKAFIPKPQ 39
++A GM R + S++ + + + P
Sbjct: 192 LLARPGMHSRSKCSVVREAFTDTKLIAISDANELKGFDSQCIEEWDPILFSAAEIWPTKG 251
Query: 40 VDVGVVHFTPRVHPIIDLPFKLIERVVSCIFRYRQKQVYKPASLLFPKRKRQLVVSLLER 99
+ +V P + V + ++ + L ++ +
Sbjct: 252 KPIALVEMDPIDFDF---DVDNWDYVTRHLMILKRTPLNTVMDSLGHGGQQYF--NSRIT 306
Query: 100 ACVKPILRPYQLSVQEFGQICLAYR 124
P L+ EF + +
Sbjct: 307 DKDLLKKCPIDLTNDEFIYLTKLFM 331
>2h1r_A Dimethyladenosine transferase, putative; SGC toronto
dimethyladenosine transferase, structural genomics,
structural genomics consortium; 1.89A {Plasmodium
falciparum}
Length = 299
Score = 75.5 bits (186), Expect = 4e-17
Identities = 25/131 (19%), Positives = 49/131 (37%), Gaps = 4/131 (3%)
Query: 1 MIATEGMEQRCRLSIMCQNWCNVDHRFTIPGKAFIPKPQVDVGVVHFTPRVHPIIDLPFK 60
M+A G RL+I + +C V + +F P P+VD +V P+ F
Sbjct: 148 MLANVGDSNYSRLTINVKLFCKVTKVCNVNRSSFNPPPKVDSVIVKLIPK-ESSFLTNFD 206
Query: 61 LIERVVSCIFRYRQKQVYKPASLLFPKRKRQLVVSLLERACVKPILRPYQLSVQEFGQIC 120
+ ++ F ++K ++ ++ + C P +++
Sbjct: 207 EWDNLLRICFSRKRKTLHAI---FKRNAVLNMLEHNYKNWCTLNKQVPVNFPFKKYCLDV 263
Query: 121 LAYRDMCEEMP 131
L + DMCE+
Sbjct: 264 LEHLDMCEKRS 274
>3uzu_A Ribosomal RNA small subunit methyltransferase A; ssgcid, seattle
structural genomics center for infectio disease; 1.75A
{Burkholderia pseudomallei}
Length = 279
Score = 74.9 bits (185), Expect = 4e-17
Identities = 23/109 (21%), Positives = 43/109 (39%), Gaps = 8/109 (7%)
Query: 12 RLSIMCQNWCNVDHRFTIPGKAFIPKPQVDVGVVHFTPRVHPIIDLP-FKLIERVVSCIF 70
RLS+M Q +D +P ++F P P+VD +V P + ++ VV+ F
Sbjct: 167 RLSVMLQYRYVMDKLIDVPPESFQPPPKVDSAIVRMIPHAPHELPAVDPAVLGEVVTAAF 226
Query: 71 RYRQKQVYKPASLLFPKRKRQLVVSLLERACVKPILRPYQLSVQEFGQI 119
R+K + +L + + R + V E+ ++
Sbjct: 227 SQRRKMLR--NTL-----GGYRDLVDFDALGFDLARRAEDIGVDEYVRV 268
>3fut_A Dimethyladenosine transferase; methyltransferase,
dimethyltransferase, dual-specific methyltransferase,
16S rRNA methyltransferase; 1.52A {Thermus thermophilus}
PDB: 3fuu_A* 3fuv_A 3fuw_A* 3fux_A*
Length = 271
Score = 72.2 bits (178), Expect = 5e-16
Identities = 23/108 (21%), Positives = 43/108 (39%), Gaps = 6/108 (5%)
Query: 12 RLSIMCQNWCNVDHRFTIPGKAFIPKPQVDVGVVHFTPRVHPIIDLPFKLIERVVSCIFR 71
L++ + + F +P AF P P+V +V TP + R+V F
Sbjct: 162 VLTLRVAHHAVAERLFDLPPGAFFPPPKVWSSLVRLTPTGAL----DDPGLFRLVEAAFG 217
Query: 72 YRQKQVYKPASLLFPKRKRQLVVSLLERACVKPILRPYQLSVQEFGQI 119
R+K + +L + V L + P +R +L ++ F ++
Sbjct: 218 KRRKTLL--NALAAAGYPKARVEEALRALGLPPRVRAEELDLEAFRRL 263
>1zq9_A Probable dimethyladenosine transferase; SGC, structural genomics,
structural genomics consortium; HET: SAM; 1.90A {Homo
sapiens} SCOP: c.66.1.24
Length = 285
Score = 70.1 bits (172), Expect = 3e-15
Identities = 31/122 (25%), Positives = 52/122 (42%), Gaps = 3/122 (2%)
Query: 1 MIATEGMEQRCRLSIMCQNWCNVDHRFTIPGKAFIPKPQVDVGVVHFTPRVHPIIDLPFK 60
++A G + CRLSI Q VDH + F P P+V+ VV P+ +P + F+
Sbjct: 135 LVAKPGDKLYCRLSINTQLLARVDHLMKVGKNNFRPPPKVESSVVRIEPK-NPPPPINFQ 193
Query: 61 LIERVVSCIFRYRQKQVYKPASLLFPKRKRQLVVSLLERACVKPILRPYQLSVQEFGQIC 120
+ +V F + K + A+ ++ L + V I+ P S+ + Q
Sbjct: 194 EWDGLVRITFVRKNKTLS--AAFKSSAVQQLLEKNYRIHCSVHNIIIPEDFSIADKIQQI 251
Query: 121 LA 122
L
Sbjct: 252 LT 253
>1yub_A Ermam, rRNA methyltransferase; MLS antibiotics; NMR {Streptococcus
pneumoniae} SCOP: c.66.1.24
Length = 245
Score = 69.5 bits (171), Expect = 3e-15
Identities = 18/108 (16%), Positives = 39/108 (36%), Gaps = 13/108 (12%)
Query: 12 RLSIMCQNWCNVDHRFTIPGKAFIPKPQVDVGVVHFTPRVHPIIDLPFKLIERVVSCIFR 71
L ++ ++ +P + F PKP+V+ ++ T + D +KL VS
Sbjct: 140 TLGLLLHTQVSIQQLLKLPAECFHPKPKVNSVLIKLTRHTTDVPDKYWKLYTYFVSKWVN 199
Query: 72 YRQKQVYKPASLLFPKRKRQLVVSLLERACVKPILRPYQLSVQEFGQI 119
+Q LF K + + + + ++ ++ I
Sbjct: 200 REYRQ-------LFTKNQFHQAMKHAK------VNNLSTITYEQVLSI 234
>3rui_A Ubiquitin-like modifier-activating enzyme ATG7; autophagosome
formation, non-canonical E1, ATP BI UBL, ATG8, ATG12,
ATG10, ATG3, UBL activation, thiolation; 1.91A
{Saccharomyces cerevisiae} PDB: 3t7e_A 3vh3_A 3vh4_A*
Length = 340
Score = 27.3 bits (61), Expect = 2.3
Identities = 14/61 (22%), Positives = 24/61 (39%), Gaps = 2/61 (3%)
Query: 100 ACVKPILRPYQLSVQEFGQICLAYRDMCEEMPGLYEYTLEDTPGDIEPEAVAEQEGEGDE 159
AC ++ + EF + L + EE+ GL E + + ++ E DE
Sbjct: 281 ACSPKVIEAFTDLGWEFVKKALEHPLYLEEISGLSVIKQEVE--RLGNDVFEWEDDESDE 338
Query: 160 I 160
I
Sbjct: 339 I 339
>3hf5_A 4-methylmuconolactone methylisomerase; ferredoxin, ferredoxin-like
fold, beta-barrel, biodegradation, ortho- cleavage; HET:
3ML; 1.40A {Pseudomonas reinekei} PDB: 3hds_A* 3hfk_A*
2ifx_A*
Length = 116
Score = 25.9 bits (56), Expect = 3.9
Identities = 10/32 (31%), Positives = 21/32 (65%)
Query: 105 ILRPYQLSVQEFGQICLAYRDMCEEMPGLYEY 136
+++P +S ++F + C+ + M MPGL++Y
Sbjct: 17 LVKPESMSHEQFRKECVVHFQMSAGMPGLHKY 48
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis,
programmed cell death; HET: DTP; 6.90A {Drosophila
melanogaster} PDB: 3iz8_A*
Length = 1221
Score = 26.4 bits (57), Expect = 6.5
Identities = 14/76 (18%), Positives = 27/76 (35%), Gaps = 15/76 (19%)
Query: 58 PFKLIERVVSCIFR-YRQKQVYKPASLLFPKRKRQLVVSLLERACVKPILRPYQ-LSVQ- 114
P + + R Y QV+ ++ + +L +LLE LRP + + +
Sbjct: 105 PSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLE-------LRPAKNVLIDG 157
Query: 115 --EFGQICLA---YRD 125
G+ +A
Sbjct: 158 VLGSGKTWVALDVCLS 173
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.325 0.142 0.443
Gapped
Lambda K H
0.267 0.0612 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,625,818
Number of extensions: 148671
Number of successful extensions: 351
Number of sequences better than 10.0: 1
Number of HSP's gapped: 341
Number of HSP's successfully gapped: 17
Length of query: 165
Length of database: 6,701,793
Length adjustment: 86
Effective length of query: 79
Effective length of database: 4,300,587
Effective search space: 339746373
Effective search space used: 339746373
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 53 (24.4 bits)