RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy6779
(144 letters)
>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} SCOP: c.116.1.1 d.79.3.3
Length = 274
Score = 131 bits (332), Expect = 6e-39
Identities = 37/147 (25%), Positives = 66/147 (44%), Gaps = 8/147 (5%)
Query: 5 KSRKQREKKGWLMLEGKRILIDALKANLKLKMVFFS-------QWDILKELPLPEDVPQH 57
RK R+ + ++EG R + AL+A ++L+ + + L +
Sbjct: 18 LERKHRDSQRRFLIEGAREIERALQAGIELEQALVWEGGLNPEEQQVYAALGRVGRLALL 77
Query: 58 RVDYKNIQLWSDLVTPPGIIGIFELPAHPIASIDPASLPLNIVCDNIRDPGNMGSILRVC 117
V ++ S P G+I + +P + P+ L +V + PGN+G++LR
Sbjct: 78 EVSEAVLKKLSVRDNPAGLIALARMPERTLEEYRPSPDALILVAVGLEKPGNLGAVLRSA 137
Query: 118 AAVGARQVVCSRGCVDIYDNKVIRAAA 144
A GA V+ + G VD+Y +VIR +
Sbjct: 138 DAAGAEAVLVA-GGVDLYSPQVIRNST 163
>2i6d_A RNA methyltransferase, TRMH family; stuctural genomics, PORP
gingivalis, knot, structural genomics, PSI-2, protein
struc initiative; HET: MSE; 1.85A {Porphyromonas
gingivalis}
Length = 257
Score = 127 bits (321), Expect = 2e-37
Identities = 39/144 (27%), Positives = 70/144 (48%), Gaps = 13/144 (9%)
Query: 5 KSRKQREKKGWLMLEGKRILIDALKANLKLKMVFFSQWDILKELPLPEDVPQHRV----D 60
+ RK R ++ +EG +++ + L +V + L+ + P D + D
Sbjct: 17 RERKYRLREQAFAVEGPKLVGEMLPFYRCRMLVGTAAM--LRAVSTPHDAEVVELPESFD 74
Query: 61 YKNIQLWSDLVTPPGIIGIFELPAHPIASIDPASLPLNIVCDNIRDPGNMGSILRVCAAV 120
+K I S TP ++ +F+LPA P ++ L ++ D ++DPGN+G+ILR
Sbjct: 75 FKRI---STQTTPQPLMAVFDLPAEPEPVVEG----LTLLLDGVQDPGNVGTILRTADWF 127
Query: 121 GARQVVCSRGCVDIYDNKVIRAAA 144
G R V G D++ KV++A+
Sbjct: 128 GIRHVWLGTGSADVFSPKVVQASM 151
>1x7o_A Avirb, rRNA methyltransferase; SPOU, C-terminal knot, seMet; 2.37A
{Streptomyces viridochromogenes} PDB: 1x7p_A*
Length = 287
Score = 126 bits (319), Expect = 6e-37
Identities = 32/145 (22%), Positives = 64/145 (44%), Gaps = 5/145 (3%)
Query: 5 KSRKQREKKGWLMLEGKRILIDALKANLKLKMVFFSQWDILKE-----LPLPEDVPQHRV 59
+R +R + G ++ G R + A++ ++ + + L + L
Sbjct: 30 GNRNKRTRAGEFLVMGVRPISLAVEHGWPVRTLLYDGQRELSKWARELLRTVRTEQIAMA 89
Query: 60 DYKNIQLWSDLVTPPGIIGIFELPAHPIASIDPASLPLNIVCDNIRDPGNMGSILRVCAA 119
++L PP ++ + E+PA + I L ++ D PGN+GSI+R A
Sbjct: 90 PDLLMELGEKNEAPPEVVAVVEMPADDLDRIPVREDFLGVLFDRPTSPGNIGSIIRSADA 149
Query: 120 VGARQVVCSRGCVDIYDNKVIRAAA 144
+GA ++ + D+YD K +R++
Sbjct: 150 LGAHGLIVAGHAADVYDPKSVRSST 174
>3nk6_A 23S rRNA methyltransferase; nosiheptide, nosiheptide-resistance
methyltransferase, 23S R methyltransferase; 2.00A
{Streptomyces actuosus} PDB: 3nk7_A* 3gyq_A*
Length = 277
Score = 109 bits (274), Expect = 3e-30
Identities = 28/143 (19%), Positives = 58/143 (40%), Gaps = 5/143 (3%)
Query: 7 RKQREKKGWLMLEGKRILIDALKANLKLKMVFFSQW----DILKELPLPEDVPQHRVDYK 62
+ R ++E L++ ++A ++ V+ S L +L ++P +D
Sbjct: 26 KHSRASIKTTLIEDTEPLMECIRAGVQFIEVYGSSGTPLDPALLDLCRQREIPVRLIDVS 85
Query: 63 NIQLWSDLVTPPGIIGIFELPAHPIASIDPASLPLNIVCDNIRDPGNMGSILRVCAAVGA 122
+ + GI +P + +V D ++ GN+G+I+R A+GA
Sbjct: 86 IVNQLFKAERKAKVFGIARVPRPARLADIAERGGDVVVLDGVKIVGNIGAIVRTSLALGA 145
Query: 123 RQVV-CSRGCVDIYDNKVIRAAA 144
+V I D +++RA+
Sbjct: 146 AGIVLVDSDLATIADRRLLRASR 168
>1v2x_A TRNA (GM18) methyltransferase; DEEP trefoil knot, riken structural
genomics/proteomics INIT RSGI, structural genomics; HET:
SAM; 1.50A {Thermus thermophilus} SCOP: c.116.1.1
Length = 194
Score = 47.5 bits (114), Expect = 1e-07
Identities = 11/49 (22%), Positives = 20/49 (40%), Gaps = 2/49 (4%)
Query: 96 PLNIVCDNIRDPGNMGSILRVCAAVGARQVVCSRGCVDIYDNKVIRAAA 144
L ++ +N+ P N+ +ILR C AVG + + +
Sbjct: 22 DLTVLLENVHKPHNLSAILRTCDAVGVLEAHAVNPTGGVP--TFNETSG 68
>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}
Length = 184
Score = 46.8 bits (112), Expect = 2e-07
Identities = 11/32 (34%), Positives = 15/32 (46%)
Query: 96 PLNIVCDNIRDPGNMGSILRVCAAVGARQVVC 127
L +V I P N+G + R C GA +V
Sbjct: 26 RLIVVASLIDKPTNLGGLCRTCEVFGASVLVV 57
>1zjr_A TRNA (guanosine-2'-O-)-methyltransferase; methylase, RNA modifying
enzyme, topological knot; 1.85A {Aquifex aeolicus}
Length = 211
Score = 43.7 bits (104), Expect = 3e-06
Identities = 11/51 (21%), Positives = 23/51 (45%), Gaps = 2/51 (3%)
Query: 96 PLNIVCDNIRDPGNMGSILRVCAAVGARQV--VCSRGCVDIYDNKVIRAAA 144
L + DN+++ N +I+R C AVG + + G + + + +
Sbjct: 25 DLIVFADNVKNEHNFSAIVRTCDAVGVLYLYYYHAEGKKAKINEGITQGSH 75
>1gz0_A Hypothetical tRNA/RRNA methyltransferase YJFH;
2'O-methyltransferase, knot, montreal- kingston
bacterial structural genomics initiative, BSGI; 2.5A
{Escherichia coli} SCOP: c.116.1.1 d.79.3.3
Length = 253
Score = 43.8 bits (104), Expect = 4e-06
Identities = 12/40 (30%), Positives = 18/40 (45%)
Query: 87 IASIDPASLPLNIVCDNIRDPGNMGSILRVCAAVGARQVV 126
I P ++ D + DP N+G+ LR A G V+
Sbjct: 96 PDLIASLDQPFLLILDGVTDPHNLGACLRSADAAGVHAVI 135
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl RED beta-ketoacyl
synthase, dehydratase; 4.00A {Saccharomyces cerevisiae}
Length = 2006
Score = 40.4 bits (94), Expect = 8e-05
Identities = 29/122 (23%), Positives = 49/122 (40%), Gaps = 35/122 (28%)
Query: 24 LIDALKANLKLKMVFFSQWDILKELPLPEDVPQHRVDYKNIQLWSDLVTPPGIIGIFELP 83
L + ++ L + VF +IL+ L P + P DY L S ++ P +IG+ +L
Sbjct: 195 LSELIRTTLDAEKVFTQGLNILEWLENPSNTPD--KDY----LLSIPISCP-LIGVIQL- 246
Query: 84 AHPIASIDPASLPLNIVCDNI-RDPGNMGSILRVCAAVGARQVVCSRGCVDIYDNKVIRA 142
AH + + + PG + S L+ GA S+G ++ A
Sbjct: 247 AHYV-----------VTAKLLGFTPGELRSYLK-----GA--TGHSQG--------LVTA 280
Query: 143 AA 144
A
Sbjct: 281 VA 282
Score = 28.1 bits (62), Expect = 1.3
Identities = 12/81 (14%), Positives = 23/81 (28%), Gaps = 29/81 (35%)
Query: 69 DLVTPPGIIGIFELPAHPIASIDPASLPLNIVCDNIRDPGNMGSIL------RVCAAVGA 122
++V G+ +P + + + +N PG + + V VG
Sbjct: 1784 EVVFYRGMTMQVAVPRDELGRSNYGMIAIN--------PGRVAASFSQEALQYVVERVGK 1835
Query: 123 R---------------QVVCS 128
R Q V +
Sbjct: 1836 RTGWLVEIVNYNVENQQYVAA 1856
>3e5y_A TRMH family RNA methyltransferase; ssgcid, protein knot, decode,
structural genomics; 2.40A {Burkholderia pseudomallei
305}
Length = 160
Score = 30.1 bits (69), Expect = 0.17
Identities = 11/27 (40%), Positives = 16/27 (59%)
Query: 97 LNIVCDNIRDPGNMGSILRVCAAVGAR 123
N+V P N G+++R+CA GAR
Sbjct: 6 FNVVLVEPEIPPNTGNVIRLCANTGAR 32
>3n4j_A RNA methyltransferase; center for structural genomics of INF
diseases, csgid; 1.47A {Yersinia pestis} PDB: 3n4k_A*
1mxi_A* 1j85_A*
Length = 165
Score = 29.7 bits (68), Expect = 0.19
Identities = 12/31 (38%), Positives = 18/31 (58%)
Query: 93 ASLPLNIVCDNIRDPGNMGSILRVCAAVGAR 123
++ LNIV P N G+I+R+CA G +
Sbjct: 1 SNAMLNIVLFEPEIPPNTGNIIRLCANTGCQ 31
>3l8u_A SMU.1707C, putative rRNA methylase; methyltransferase, knotted
protein; 2.00A {Streptococcus mutans}
Length = 182
Score = 29.1 bits (66), Expect = 0.37
Identities = 9/28 (32%), Positives = 13/28 (46%)
Query: 96 PLNIVCDNIRDPGNMGSILRVCAAVGAR 123
++V + P N G+I R CAA
Sbjct: 17 RNHVVLFQPQIPANTGNIARTCAATNTS 44
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna;
HET: CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 27.2 bits (59), Expect = 1.7
Identities = 10/48 (20%), Positives = 15/48 (31%), Gaps = 28/48 (58%)
Query: 8 KQREKKGWLMLEGKRILIDALKANLKLKMVFFSQWDILKELPLPEDVP 55
KQ KK L+A+LKL ++ + P
Sbjct: 19 KQALKK--------------LQASLKL----YA----------DDSAP 38
>2pv7_A T-protein [includes: chorismate mutase (EC 5.4.99 and prephenate
dehydrogenase (EC...; 1574749, chorismate mutase type
II; HET: MSE TYR NAD; 2.00A {Haemophilus influenzae}
SCOP: a.100.1.12 c.2.1.6
Length = 298
Score = 26.5 bits (59), Expect = 3.3
Identities = 12/48 (25%), Positives = 19/48 (39%), Gaps = 1/48 (2%)
Query: 82 LPAHPIASIDPASLP-LNIVCDNIRDPGNMGSILRVCAAVGARQVVCS 128
L HP+ D AS+ +V + R P +L GA+ +
Sbjct: 118 LGLHPMFGADIASMAKQVVVRCDGRFPERYEWLLEQIQIWGAKIYQTN 165
>1upq_A PEPP1; PH domain, phosphoinositide binding, signal transduction;
1.48A {Homo sapiens} SCOP: b.55.1.1 PDB: 1upr_A*
Length = 123
Score = 25.5 bits (56), Expect = 5.0
Identities = 8/37 (21%), Positives = 13/37 (35%)
Query: 3 YMKSRKQREKKGWLMLEGKRILIDALKANLKLKMVFF 39
Y K ++ G ++L I D A + F
Sbjct: 42 YYKDSREESVLGSVLLPSYNIRPDGPGAPRGRRFTFT 78
>3p8c_A Cytoplasmic FMR1-interacting protein 1; actin polymerization,
protein binding; 2.29A {Homo sapiens}
Length = 1253
Score = 25.9 bits (56), Expect = 5.9
Identities = 9/17 (52%), Positives = 12/17 (70%)
Query: 39 FSQWDILKELPLPEDVP 55
S D+L+ELPLP+ P
Sbjct: 11 LSNVDLLEELPLPDQQP 27
>2z1d_A Hydrogenase expression/formation protein HYPD; [NIFE] hydrogenase
maturation, [4Fe-4S] cluster, thiol redox binding
protein; HET: CSW; 2.07A {Thermococcus kodakarensis}
Length = 372
Score = 25.4 bits (56), Expect = 7.9
Identities = 11/61 (18%), Positives = 18/61 (29%), Gaps = 7/61 (11%)
Query: 71 VTPPGIIGIFELPAHPIASIDPASLPLNIVC---DNIRDPGNMGSILRVCAAVGARQVVC 127
+TP I I I+ D + P MGS + + ++V
Sbjct: 70 ITPVEDIVA----MQLIMRKAREEGEEIILTTFGDMYKIPTPMGSFADLKSEGFDVRIVY 125
Query: 128 S 128
Sbjct: 126 G 126
>2a14_A Indolethylamine N-methyltransferase; SGC,INMT, structural genomics,
structural genomics consortium; HET: SAH; 1.70A {Homo
sapiens} SCOP: c.66.1.15
Length = 263
Score = 25.0 bits (54), Expect = 9.7
Identities = 8/42 (19%), Positives = 14/42 (33%)
Query: 15 WLMLEGKRILIDALKANLKLKMVFFSQWDILKELPLPEDVPQ 56
LEG + + L+ + + D+ PL V
Sbjct: 114 ACELEGNSGRWEEKEEKLRAAVKRVLKCDVHLGNPLAPAVLP 155
>2dkp_A Pleckstrin homology domain-containing family A member 5; PH
domain, pleckstrin homology domain-containing protein
family A member 5; NMR {Homo sapiens}
Length = 128
Score = 24.7 bits (54), Expect = 9.9
Identities = 7/36 (19%), Positives = 16/36 (44%)
Query: 3 YMKSRKQREKKGWLMLEGKRILIDALKANLKLKMVF 38
Y + K+ G ++L +I + + ++ K F
Sbjct: 52 YYRDEKEEGILGSILLPSFQIALLTSEDHINRKYAF 87
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
0.324 0.141 0.438
Gapped
Lambda K H
0.267 0.0495 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,376,701
Number of extensions: 140247
Number of successful extensions: 337
Number of sequences better than 10.0: 1
Number of HSP's gapped: 327
Number of HSP's successfully gapped: 35
Length of query: 144
Length of database: 6,701,793
Length adjustment: 85
Effective length of query: 59
Effective length of database: 4,328,508
Effective search space: 255381972
Effective search space used: 255381972
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: 41 (22.0 bits)
S2: 52 (24.4 bits)