RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy4127
(75 letters)
>2dul_A N(2),N(2)-dimethylguanosine tRNA methyltransferas; tRNA
modification enzyme, guanine 26, N(2),N(2)-dimethyltran
structural genomics; 1.90A {Pyrococcus horikoshii} SCOP:
c.66.1.58 PDB: 2ejt_A* 2eju_A* 2ytz_A*
Length = 378
Score = 84.5 bits (208), Expect = 2e-21
Identities = 36/69 (52%), Positives = 43/69 (62%)
Query: 7 RGRHFDAIDLDPFGNPTRFLDAAVSSLRDGGLLLVTCTDMAVLCGNTPETCYVKYNAVSL 66
R R+F IDLDPFG+P FLD A+ S + G+L VT TD A LCG P C KY AV L
Sbjct: 128 RHRYFHFIDLDPFGSPMEFLDTALRSAKRRGILGVTATDGAPLCGAHPRACLRKYLAVPL 187
Query: 67 KTAACHEMP 75
+ CHE+
Sbjct: 188 RGELCHEVG 196
>3axs_A Probable N(2),N(2)-dimethylguanosine tRNA methylt TRM1; structural
genomics, riken structural genomics/proteomics in RSGI;
HET: SFG; 2.16A {Aquifex aeolicus} PDB: 3axt_A*
Length = 392
Score = 75.3 bits (184), Expect = 4e-18
Identities = 31/75 (41%), Positives = 43/75 (57%)
Query: 1 MQLEKIRGRHFDAIDLDPFGNPTRFLDAAVSSLRDGGLLLVTCTDMAVLCGNTPETCYVK 60
L K G FD +DLDPFG P F+++ S++ GG+L +T TD A L G P+TC +
Sbjct: 116 FFLRKEWGFGFDYVDLDPFGTPVPFIESVALSMKRGGILSLTATDTAPLSGTYPKTCMRR 175
Query: 61 YNAVSLKTAACHEMP 75
Y A L+ HE+
Sbjct: 176 YMARPLRNEFKHEVG 190
>2igt_A SAM dependent methyltransferase; alpha-beta sandwich, beta-barrel,
structural genomics, PSI-2 structure initiative; HET:
MSE SAM GOL; 1.89A {Agrobacterium tumefaciens str} SCOP:
c.66.1.51
Length = 332
Score = 33.6 bits (77), Expect = 0.002
Identities = 16/55 (29%), Positives = 18/55 (32%), Gaps = 14/55 (25%)
Query: 4 EKIRGRHFDAIDLDP--FGNPTR------------FLDAAVSSLRDGGLLLVTCT 44
E+ RG +D I DP FG T LD L L LV
Sbjct: 219 EERRGSTYDIILTDPPKFGRGTHGEVWQLFDHLPLMLDICREILSPKALGLVLTA 273
>2yx1_A Hypothetical protein MJ0883; methyl transferase, tRNA modification
enzyme, transferase; HET: SFG; 2.20A {Methanocaldococcus
jannaschii} PDB: 2zzn_A* 3ay0_A* 2zzm_A*
Length = 336
Score = 29.8 bits (67), Expect = 0.050
Identities = 5/36 (13%), Positives = 16/36 (44%)
Query: 8 GRHFDAIDLDPFGNPTRFLDAAVSSLRDGGLLLVTC 43
+ + ++ +F+D A+ + +GG++
Sbjct: 256 DVKGNRVIMNLPKFAHKFIDKALDIVEEGGVIHYYT 291
>2frn_A Hypothetical protein PH0793; structural genomics, PSI, protein
structure initiative, midwest center for structural
genomics, MCSG; 2.10A {Pyrococcus horikoshii OT3} SCOP:
c.66.1.47 PDB: 3k6r_A 3a25_A* 3a26_A*
Length = 278
Score = 28.4 bits (63), Expect = 0.16
Identities = 8/39 (20%), Positives = 14/39 (35%)
Query: 6 IRGRHFDAIDLDPFGNPTRFLDAAVSSLRDGGLLLVTCT 44
D I + F+ A+S +DG ++ T
Sbjct: 188 PGENIADRILMGYVVRTHEFIPKALSIAKDGAIIHYHNT 226
>3dr5_A Putative O-methyltransferase; Q8NRD3, CGL1119, PF01596, CGR117,
NESG, structural genomics, PSI-2, protein structure
initiative; 2.25A {Corynebacterium glutamicum}
Length = 221
Score = 28.4 bits (64), Expect = 0.16
Identities = 9/41 (21%), Positives = 17/41 (41%), Gaps = 3/41 (7%)
Query: 3 LEKIRGRHFDA--IDLDPFGNPTRFLDAAVSSLRDGGLLLV 41
+ ++ + + P +DAA LR GG L++
Sbjct: 122 MSRLANDSYQLVFGQVSPMDLK-ALVDAAWPLLRRGGALVL 161
>1sqg_A SUN protein, FMU protein; rossmann-fold, mixed beta sheet,
methyltransferase-fold, RNA-binding domain; 1.65A
{Escherichia coli} SCOP: a.79.1.3 c.66.1.38 PDB: 1sqf_A
Length = 429
Score = 27.9 bits (63), Expect = 0.24
Identities = 9/22 (40%), Positives = 12/22 (54%), Gaps = 1/22 (4%)
Query: 24 RFLDAAVSSLRDGGLLL-VTCT 44
LDA L+ GG L+ TC+
Sbjct: 355 EILDAIWPHLKTGGTLVYATCS 376
>3p9n_A Possible methyltransferase (methylase); RV2966C, adoMet binding,
RNA methylase, RSMD, SAM-fold, RNA methyltransferase;
1.90A {Mycobacterium tuberculosis}
Length = 189
Score = 27.1 bits (61), Expect = 0.36
Identities = 7/38 (18%), Positives = 15/38 (39%), Gaps = 1/38 (2%)
Query: 3 LEKIRGRHFDAIDLD-PFGNPTRFLDAAVSSLRDGGLL 39
+ D + D P+ + +DA +++L G
Sbjct: 106 VAAGTTSPVDLVLADPPYNVDSADVDAILAALGTNGWT 143
>3a27_A TYW2, uncharacterized protein MJ1557; wybutosine modification,
transferase; HET: SAM; 2.00A {Methanocaldococcus
jannaschii}
Length = 272
Score = 27.3 bits (60), Expect = 0.37
Identities = 8/36 (22%), Positives = 14/36 (38%)
Query: 9 RHFDAIDLDPFGNPTRFLDAAVSSLRDGGLLLVTCT 44
D + + +FLD L+D G++ T
Sbjct: 185 DVADRVIMGYVHKTHKFLDKTFEFLKDRGVIHYHET 220
>1nkv_A Hypothetical protein YJHP; structural genomics, PSI, protein
structure initiative, northeast structural genomics
consortium, NESG; 2.90A {Escherichia coli} SCOP:
c.66.1.21
Length = 256
Score = 27.4 bits (61), Expect = 0.38
Identities = 10/55 (18%), Positives = 17/55 (30%), Gaps = 15/55 (27%)
Query: 4 EKIRGRHFDAIDLDP---------------FGNPTRFLDAAVSSLRDGGLLLVTC 43
E++ H DA G + SL+ GG++L+
Sbjct: 86 ERVHFIHNDAAGYVANEKCDVAACVGATWIAGGFAGAEELLAQSLKPGGIMLIGE 140
>2yxl_A PH0851 protein, 450AA long hypothetical FMU protein; FMU-homolog,
methyltransferase, structural genomics, NPPSFA; HET:
SFG; 2.55A {Pyrococcus horikoshii}
Length = 450
Score = 26.5 bits (59), Expect = 0.87
Identities = 8/20 (40%), Positives = 13/20 (65%), Gaps = 1/20 (5%)
Query: 26 LDAAVSSLRDGGLLL-VTCT 44
L++A ++ GG LL TC+
Sbjct: 372 LESAARLVKPGGRLLYTTCS 391
>3gjy_A Spermidine synthase; APC62791, structural genomics, PSI-2, protein
structure initiative; HET: MSE; 1.47A {Corynebacterium
glutamicum atcc 13032}
Length = 317
Score = 26.5 bits (58), Expect = 0.91
Identities = 12/51 (23%), Positives = 15/51 (29%), Gaps = 8/51 (15%)
Query: 3 LEKIRGRHFDAI--DL-DPFGNP-----TRFLDAAVSSLRDGGLLLVTCTD 45
E D I D+ P F + L GGL + C D
Sbjct: 152 AESFTPASRDVIIRDVFAGAITPQNFTTVEFFEHCHRGLAPGGLYVANCGD 202
>3dli_A Methyltransferase; PSI-II, NYSGXRC, structural genomics, protein
structure initiative; 2.46A {Archaeoglobus fulgidus}
Length = 240
Score = 26.0 bits (57), Expect = 1.1
Identities = 4/47 (8%), Positives = 15/47 (31%), Gaps = 6/47 (12%)
Query: 3 LEKIRGRHFDAIDLD------PFGNPTRFLDAAVSSLRDGGLLLVTC 43
L+ + ++ D + + L S ++ +++
Sbjct: 94 LKSLPDKYLDGVMISHFVEHLDPERLFELLSLCYSKMKYSSYIVIES 140
>3ajd_A Putative methyltransferase MJ0026; tRNA, M5C, rossmann fold,
structural genomics, riken structu genomics/proteomics
initiative; 1.27A {Methanocaldococcus jannaschii} PDB:
3a4t_A
Length = 274
Score = 25.6 bits (57), Expect = 1.3
Identities = 6/20 (30%), Positives = 11/20 (55%), Gaps = 1/20 (5%)
Query: 26 LDAAVSSLRDGGLLL-VTCT 44
+D + L+ G L+ TC+
Sbjct: 194 IDIGIDLLKKDGELVYSTCS 213
>3lvj_C Sulfurtransferase TUSA; protein-protein complex, structural
genomics, montreal-kings bacterial structural genomics
initiative, BSGI; HET: PLP; 2.44A {Escherichia coli}
PDB: 3lvk_B* 1dcj_A
Length = 82
Score = 25.3 bits (56), Expect = 1.3
Identities = 12/45 (26%), Positives = 17/45 (37%), Gaps = 14/45 (31%)
Query: 17 DPFGNPTRFLDA--------------AVSSLRDGGLLLVTCTDMA 47
D F +P LDA V +++ G LL+ D A
Sbjct: 4 DLFSSPDHTLDALGLRCPEPVMMVRKTVRNMQPGETLLIIADDPA 48
>3ntv_A MW1564 protein; rossmann fold, putative methyltransferase,
transferase; HET: MSE; 1.55A {Staphylococcus aureus}
Length = 232
Score = 25.3 bits (56), Expect = 1.8
Identities = 8/41 (19%), Positives = 17/41 (41%), Gaps = 3/41 (7%)
Query: 3 LEKIRGRHFDA--IDLDPFGNPTRFLDAAVSSLRDGGLLLV 41
E + + +D ID + +F + L+ GL++
Sbjct: 135 FENVNDKVYDMIFIDAAKAQSK-KFFEIYTPLLKHQGLVIT 174
>3mcq_A Thiamine-monophosphate kinase; structural genomics, joint center
for structural genomics, J protein structure
initiative, PSI-2; HET: MSE PGE PG4 1PE; 1.91A
{Methylobacillus flagellatus}
Length = 319
Score = 25.2 bits (56), Expect = 1.9
Identities = 9/22 (40%), Positives = 11/22 (50%), Gaps = 1/22 (4%)
Query: 27 DAAVSSLRDGGLLLVTCTDMAV 48
DAA+ G L V+ DM V
Sbjct: 27 DAALIQPSPGMELAVS-ADMLV 47
>2b78_A Hypothetical protein SMU.776; structure genomics,
methyltransferase, caries, structural genomics, unknown
function; 2.00A {Streptococcus mutans} SCOP: b.122.1.9
c.66.1.51 PDB: 3ldf_A*
Length = 385
Score = 25.3 bits (56), Expect = 2.0
Identities = 9/54 (16%), Positives = 18/54 (33%), Gaps = 20/54 (37%)
Query: 7 RGRHFDAIDLDPFGNPT----------------RFLDAAVSSLRDGGLLLVTCT 44
+D I +DP P+ + + + L + G L++ T
Sbjct: 282 HHLTYDIIIIDP---PSFARNKKEVFSVSKDYHKLIRQGLEILSENG-LIIAST 331
>1dus_A MJ0882; hypothetical protein, methanococcus jannaschii, structural
genomics, BSGC structure funded by NIH; 1.80A
{Methanocaldococcus jannaschii} SCOP: c.66.1.4
Length = 194
Score = 24.6 bits (54), Expect = 3.0
Identities = 10/48 (20%), Positives = 18/48 (37%), Gaps = 13/48 (27%)
Query: 3 LEKIRGRHFDAIDLDPFGNP---------TRFLDAAVSSLRDGGLLLV 41
E ++ R ++ I NP R ++ L+D G + V
Sbjct: 112 YENVKDRKYNKI----ITNPPIRAGKEVLHRIIEEGKELLKDNGEIWV 155
>1zcd_A Na(+)/H(+) antiporter 1; membrane protein; 3.45A {Escherichia
coli} PDB: 3fi1_A
Length = 388
Score = 24.5 bits (54), Expect = 4.3
Identities = 5/19 (26%), Positives = 12/19 (63%)
Query: 36 GGLLLVTCTDMAVLCGNTP 54
GG++L+ +A++ N+
Sbjct: 14 GGIILIIAAILAMIMANSG 32
>1k7j_A Protein YCIO, protein TF1; structural genomics, X-RAY
crystallography, putative translation factor, PSI,
protein structure initiative; 1.40A {Escherichia coli}
SCOP: d.115.1.1 PDB: 1kk9_A
Length = 206
Score = 24.4 bits (54), Expect = 4.3
Identities = 7/25 (28%), Positives = 12/25 (48%)
Query: 14 IDLDPFGNPTRFLDAAVSSLRDGGL 38
+ P R ++ AV +R GG+
Sbjct: 5 FYIHPDNPQQRLINQAVEIVRKGGV 29
>2cjg_A L-lysine-epsilon aminotransferase; internal aldimine, pyridoxal
phosphate, PLP, RV3290C, lysine amino transferase; HET:
PMP; 1.95A {Mycobacterium tuberculosis} PDB: 2cjd_A*
2cin_A* 2cjh_A* 2jjg_A* 2jje_A* 2jjh_A* 2jjf_A
Length = 449
Score = 24.5 bits (54), Expect = 4.3
Identities = 6/44 (13%), Positives = 12/44 (27%), Gaps = 5/44 (11%)
Query: 6 IRGR-HFDAIDLDPFGNPTRFLDAAVSSLRDGGLLLVTCTDMAV 48
RGR A L + + ++++ V
Sbjct: 382 PRGRGLMCAFSLPTTADRDELIRQL----WQRAVIVLPAGADTV 421
>3fpf_A Mtnas, putative uncharacterized protein; thermonicotianamine,
nicotianamine, biosynthetic protein; HET: TNA MTA; 1.66A
{Methanothermobacter thermautotrophicusorganism_taxid}
PDB: 3fpe_A* 3fph_A* 3fpg_A* 3fpj_A* 3o31_A*
Length = 298
Score = 24.4 bits (52), Expect = 4.7
Identities = 7/64 (10%), Positives = 25/64 (39%), Gaps = 10/64 (15%)
Query: 1 MQLEKIRGRHFDAIDLDPFGNPTRFLDAAVSSLRDGGLLLVTCTDMAVLCGNTPETCYVK 60
+ L + G + ++++P + + + G+ V V+ G+ ++
Sbjct: 139 ILLSHVYGMRVNVVEIEP-----DIAELSRKVIEGLGVDGVN-----VITGDETVIDGLE 188
Query: 61 YNAV 64
++ +
Sbjct: 189 FDVL 192
>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 = 24.2 bits (52), Expect = 5.1
Identities = 5/24 (20%), Positives = 8/24 (33%), Gaps = 4/24 (16%)
Query: 53 TPETCYVKYNAVSLK----TAACH 72
TP+ Y+ +S H
Sbjct: 225 TPDKDYLLSIPISCPLIGVIQLAH 248
>3hm2_A Precorrin-6Y C5,15-methyltransferase; alpha-beta-sandwich,
structural genomics, PSI-2, protein structure
initiative; 2.21A {Corynebacterium diphtheriae}
Length = 178
Score = 24.0 bits (52), Expect = 5.2
Identities = 8/33 (24%), Positives = 10/33 (30%)
Query: 11 FDAIDLDPFGNPTRFLDAAVSSLRDGGLLLVTC 43
D I + AA L GG L+
Sbjct: 95 PDVIFIGGGLTAPGVFAAAWKRLPVGGRLVANA 127
>4dmg_A Putative uncharacterized protein TTHA1493; rRNA, methyltransferase,
S-adenosyl-methionine, 23S ribosoma transferase; HET:
SAM; 1.70A {Thermus thermophilus}
Length = 393
Score = 23.8 bits (52), Expect = 5.8
Identities = 10/53 (18%), Positives = 15/53 (28%), Gaps = 20/53 (37%)
Query: 8 GRHFDAIDLDPFGNPT----------------RFLDAAVSSLRDGGLLLVTCT 44
F + LDP PT + A+ L + G L +
Sbjct: 278 EGPFHHVLLDP---PTLVKRPEELPAMKRHLVDLVREALRLLAEEG-FLWLSS 326
>2kw5_A SLR1183 protein; structural genomics, northeast structural genomics
consortium (NESG), PSI-2, protein structure initiative,
unknown function; NMR {Synechocystis} PDB: 3mer_A
Length = 202
Score = 23.3 bits (50), Expect = 8.9
Identities = 7/55 (12%), Positives = 14/55 (25%), Gaps = 16/55 (29%)
Query: 5 KIRGRHFDAIDLDPFGNP----------------TRFLDAAVSSLRDGGLLLVTC 43
KI + D D + + L+ GG+ ++
Sbjct: 77 KITTVQSNLADFDIVADAWEGIVSIFCHLPSSLRQQLYPKVYQGLKPGGVFILEG 131
>3fd5_A Selenide, water dikinase 1; selenophosphate synthetase, SELD,
ATP-binding, nucleotide-binding, selenium, transferase;
HET: AP2; 1.90A {Homo sapiens} PDB: 3fd6_A*
Length = 394
Score = 23.3 bits (50), Expect = 9.1
Identities = 16/47 (34%), Positives = 19/47 (40%), Gaps = 3/47 (6%)
Query: 3 LEKIRGRHFDAIDLDPFGNPTRFL---DAAVSSLRDGGLLLVTCTDM 46
LE ++ HF + R D V LR GGL LV TD
Sbjct: 44 LESLQENHFQEDEQFLGAVMPRLGIGMDTCVIPLRHGGLSLVQTTDY 90
>2fq6_A Cystathionine beta-lyase; protein-inhibitor complex, PLP cofactor
covalently bound to inhibitor; HET: P3F; 1.78A
{Escherichia coli} SCOP: c.67.1.3 PDB: 2gqn_A* 1cl1_A*
1cl2_A*
Length = 415
Score = 23.3 bits (51), Expect = 9.6
Identities = 10/39 (25%), Positives = 14/39 (35%), Gaps = 9/39 (23%)
Query: 20 GNPTRF-LDAAVSSLRDG--------GLLLVTCTDMAVL 49
G T F L A+ L G G V + +A +
Sbjct: 80 GTLTHFSLQQAMCELEGGAGCVLFPCGAAAVANSILAFI 118
>3c3p_A Methyltransferase; NP_951602.1, structural genomics, joint for
structural genomics, JCSG, protein structure initiative
transferase; 1.90A {Geobacter sulfurreducens pca}
Length = 210
Score = 23.3 bits (51), Expect = 9.8
Identities = 8/33 (24%), Positives = 11/33 (33%), Gaps = 3/33 (9%)
Query: 11 FDA--IDLDPFGNPTRFLDAAVSSLRDGGLLLV 41
D +D D F L+ L LL+
Sbjct: 127 IDILFMDCDVFNGA-DVLERMNRCLAKNALLIA 158
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 0.138 0.430
Gapped
Lambda K H
0.267 0.0728 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,182,190
Number of extensions: 57048
Number of successful extensions: 265
Number of sequences better than 10.0: 1
Number of HSP's gapped: 265
Number of HSP's successfully gapped: 30
Length of query: 75
Length of database: 6,701,793
Length adjustment: 44
Effective length of query: 31
Effective length of database: 5,473,269
Effective search space: 169671339
Effective search space used: 169671339
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 (21.5 bits)
S2: 51 (23.4 bits)