RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy13086
(169 letters)
>2vdv_E TRNA (guanine-N(7)-)-methyltransferase; S-adenosyl-L-methionine,
phosphorylation, M7G, spout MT, tRNA processing; HET:
SAM; 2.30A {Saccharomyces cerevisiae} PDB: 2vdu_E
Length = 246
Score = 158 bits (402), Expect = 2e-49
Identities = 95/205 (46%), Positives = 113/205 (55%), Gaps = 41/205 (20%)
Query: 1 MDWSPLYPELKDPTCE---KKVEFVDVGCGK----LYL-PMFPSTLILGLEIRVKVSDYV 52
MDWS LYP K+ KKV D+GCG + L P FP LILG+EIRV+V++YV
Sbjct: 30 MDWSKLYPYYKNAENGQMTKKVTIADIGCGFGGLMIDLSPAFPEDLILGMEIRVQVTNYV 89
Query: 53 IDEWSLY--------------------------------LKKMFFLYPDPHFKRCKYKWR 80
D L KMFF +PDPHFK+ K+K R
Sbjct: 90 EDRIIALRNNTASKHGFQNINVLRGNAMKFLPNFFEKGQLSKMFFCFPDPHFKQRKHKAR 149
Query: 81 IINQNLLSEYAYVLSEGGIVYTITDVKDLHDWIVSHFTEHPLFVECDLEELKRTDPVVDK 140
II LLSEYAYVL EGG+VYTITDVKDLH+W+V H EHPLF E + D V
Sbjct: 150 IITNTLLSEYAYVLKEGGVVYTITDVKDLHEWMVKHLEEHPLFERLSKEWEEN-DECVKI 208
Query: 141 LYQSTEEGQKVTRNKGEKFCAVFRR 165
+ +TEEG+KV R KG+KF A F R
Sbjct: 209 MRNATEEGKKVERKKGDKFVACFTR 233
>3ckk_A TRNA (guanine-N(7)-)-methyltransferase; mettl1,
S-adenosyl-L-methionine, tRNA Pro structural genomics,
structural genomics consortium, SGC; HET: SAM; 1.55A
{Homo sapiens}
Length = 235
Score = 154 bits (392), Expect = 4e-48
Identities = 107/216 (49%), Positives = 123/216 (56%), Gaps = 52/216 (24%)
Query: 1 MDWSPLYPELKDPTCE----------------KKVEFVDVGCGK-LYL----PMFPSTLI 39
MDWS LYPE P + +VEF D+GCG L P+FP TLI
Sbjct: 14 MDWSELYPEFFAPLTQNQSHDDPKDKKEKRAQAQVEFADIGCGYGGLLVELSPLFPDTLI 73
Query: 40 LGLEIRVKVSDYVIDEWSLY------------------------------LKKMFFLYPD 69
LGLEIRVKVSDYV D L KMFFL+PD
Sbjct: 74 LGLEIRVKVSDYVQDRIRALRAAPAGGFQNIACLRSNAMKHLPNFFYKGQLTKMFFLFPD 133
Query: 70 PHFKRCKYKWRIINQNLLSEYAYVLSEGGIVYTITDVKDLHDWIVSHFTEHPLFVECDLE 129
PHFKR K+KWRII+ LL+EYAYVL GG+VYTITDV +LHDW+ +HF EHPLF LE
Sbjct: 134 PHFKRTKHKWRIISPTLLAEYAYVLRVGGLVYTITDVLELHDWMCTHFEEHPLFERVPLE 193
Query: 130 ELKRTDPVVDKLYQSTEEGQKVTRNKGEKFCAVFRR 165
+L DPVV L STEEG+KV RN G+ F A+FRR
Sbjct: 194 DL-SEDPVVGHLGTSTEEGKKVLRNGGKNFPAIFRR 228
>3dxy_A TRNA (guanine-N(7)-)-methyltransferase; rossmann fold
methyltransferase, tRNA modification,
S-adenosyl-L-methionine, TR processing; HET: SAM; 1.50A
{Escherichia coli} PDB: 3dxx_A* 3dxz_A*
Length = 218
Score = 55.8 bits (135), Expect = 3e-10
Identities = 14/69 (20%), Positives = 26/69 (37%), Gaps = 10/69 (14%)
Query: 60 LKKMFFLYPDP-----HFKRCKYKWRIINQNLLSEYAYVLSEGGIVYTITDVKDLHDWIV 114
L+ + +PDP H KR RI+ L GG+ + TD + + ++
Sbjct: 106 LRMVQLFFPDPWHKARHNKR-----RIVQVPFAELVKSKLQLGGVFHMATDWEPYAEHML 160
Query: 115 SHFTEHPLF 123
+ +
Sbjct: 161 EVMSSIDGY 169
>1yzh_A TRNA (guanine-N(7)-)-methyltransferase; alpha-beta-alpha sandwich,
S-adenosylmeth dependent, structural genomics, PSI;
2.02A {Streptococcus pneumoniae} SCOP: c.66.1.53
Length = 214
Score = 54.6 bits (132), Expect = 8e-10
Identities = 15/77 (19%), Positives = 38/77 (49%)
Query: 60 LKKMFFLYPDPHFKRCKYKWRIINQNLLSEYAYVLSEGGIVYTITDVKDLHDWIVSHFTE 119
+ +++ + DP K+ K R+ + L + +L E G ++ TD + L ++ + F++
Sbjct: 112 IDRLYLNFSDPWPKKRHEKRRLTYKTFLDTFKRILPENGEIHFKTDNRGLFEYSLVSFSQ 171
Query: 120 HPLFVECDLEELKRTDP 136
+ + + +L +D
Sbjct: 172 YGMKLNGVWLDLHASDF 188
>2fca_A TRNA (guanine-N(7)-)-methyltransferase; 2.10A {Bacillus subtilis}
SCOP: c.66.1.53
Length = 213
Score = 53.4 bits (129), Expect = 2e-09
Identities = 18/77 (23%), Positives = 41/77 (53%)
Query: 60 LKKMFFLYPDPHFKRCKYKWRIINQNLLSEYAYVLSEGGIVYTITDVKDLHDWIVSHFTE 119
+K+++ + DP K+ K R+ + L +Y V+ +GG ++ TD + L ++ + F+E
Sbjct: 109 VKRVYLNFSDPWPKKRHEKRRLTYSHFLKKYEEVMGKGGSIHFKTDNRGLFEYSLKSFSE 168
Query: 120 HPLFVECDLEELKRTDP 136
+ L + +L ++
Sbjct: 169 YGLLLTYVSLDLHNSNL 185
>3mq2_A 16S rRNA methyltransferase; methyltranferase, ribosomal, antibiotic
resistance, aminoglycoside, S-adenosyl-L-methionine;
HET: SAH; 1.69A {Streptomyces SP}
Length = 218
Score = 34.7 bits (79), Expect = 0.007
Identities = 11/73 (15%), Positives = 19/73 (26%), Gaps = 4/73 (5%)
Query: 62 KMFFLYPDPHFKRCKYKWRIINQNLLSEYAYVLSEGGIVYTITDVKDLHDWIVSHFTEHP 121
++ L P R + +L A V G ++ + EHP
Sbjct: 101 ELHVLMPWGSLLR---GVLGSSPEMLRGMAAVCRPGASFLVALNLHAWRPSV-PEVGEHP 156
Query: 122 LFVECDLEELKRT 134
+E
Sbjct: 157 EPTPDSADEWLAP 169
>3p2e_A 16S rRNA methylase; methyltransferase, transferase, NPMA; HET: SAH;
1.68A {Escherichia coli} PDB: 3p2i_A 3p2k_A* 3pb3_A*
3mte_A*
Length = 225
Score = 34.8 bits (79), Expect = 0.007
Identities = 16/133 (12%), Positives = 34/133 (25%), Gaps = 34/133 (25%)
Query: 22 VDVGCGK-----LYLPMFPSTLILGLEIRVKVSDYVI----------------------- 53
+D+G G +T +G++ + +
Sbjct: 29 IDLGTGDGRNIYKLAINDQNTFYIGIDPVKENLFDISKKIIKKPSKGGLSNVVFVIAAAE 88
Query: 54 ---DEWSLYLKKMFFLYPDPHFKRCKYKWRIINQNLLSEYAYVLSEGGIVYTITDVKDLH 110
E + L+P N+++LS A + + +T D +
Sbjct: 89 SLPFELKNIADSISILFPWGTLLEYV---IKPNRDILSNVADLAKKEAHFEFVTTYSDSY 145
Query: 111 DWIVSHFTEHPLF 123
+ PL
Sbjct: 146 EEAEIKKRGLPLL 158
>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 = 33.1 bits (75), Expect = 0.038
Identities = 32/172 (18%), Positives = 55/172 (31%), Gaps = 57/172 (33%)
Query: 41 GLEIRVKVSDYVIDEWSLYLKKMFFLYPDPHFKRCKYKWRI---INQNLLSEYAYVLSEG 97
G+++ K S D W + D HFK Y + I + N ++ + E
Sbjct: 1632 GMDLY-KTSKAAQDVW----NRA-----DNHFKD-TYGFSILDIVINNPVNLTIHFGGEK 1680
Query: 98 G---------IVY-TITDVKDLHDWIVSHFTEHPLFV--ECDLEELKRTD---P---VVD 139
G +++ TI D K + I EH + L T P +++
Sbjct: 1681 GKRIRENYSAMIFETIVDGKLKTEKIFKEINEHSTSYTFRSEKGLLSATQFTQPALTLME 1740
Query: 140 K-LYQSTEEGQKVTRNK-------GEKFCA----------------VFRRGR 167
K ++ + + + GE + A VF RG
Sbjct: 1741 KAAFEDLKSKGLIPADATFAGHSLGE-YAALASLADVMSIESLVEVVFYRGM 1791
Score = 26.6 bits (58), Expect = 6.3
Identities = 23/142 (16%), Positives = 46/142 (32%), Gaps = 42/142 (29%)
Query: 28 KLYLPMFPSTLILGLEIRVKVSDYVIDEWSLYLKKMFFLYPDPHFKRCKYKWRII----- 82
L L F + + G +I + + + + +K + + RI+
Sbjct: 85 NLCLTEFENCYLEGNDIHALAAKLLQENDTTLVKTKELI-------KNYITARIMAKRPF 137
Query: 83 ---NQNLLSEYAYVLSEGGI-VYTI-----------TDVKDLHDWIVSHFTEHPL---FV 124
+ + L EG + I +++DL+ T H L +
Sbjct: 138 DKKSNSALFRAV---GEGNAQLVAIFGGQGNTDDYFEELRDLYQ------TYHVLVGDLI 188
Query: 125 E---CDLEELKRTDPVVDKLYQ 143
+ L EL RT +K++
Sbjct: 189 KFSAETLSELIRTTLDAEKVFT 210
>2ex5_A DNA endonuclease I-CEUI; homing endonuclease, laglidadg, homodimer,
protein/DNA complex, hydrolase/DNA complex; HET: DNA;
2.20A {Chlamydomonas eugametos}
Length = 207
Score = 28.1 bits (62), Expect = 1.4
Identities = 5/29 (17%), Positives = 15/29 (51%)
Query: 95 SEGGIVYTITDVKDLHDWIVSHFTEHPLF 123
S +V TI + + L + ++ + ++ +
Sbjct: 115 SNATLVLTIDNRQSLEEKVIPFYEQYVVA 143
>3ne5_A Cation efflux system protein CUSA; transmembrane helix, metal
transport; 2.90A {Escherichia coli} PDB: 3k07_A 3k0i_A
3kso_A 3kss_A
Length = 1054
Score = 28.3 bits (64), Expect = 1.6
Identities = 7/25 (28%), Positives = 13/25 (52%)
Query: 90 YAYVLSEGGIVYTITDVKDLHDWIV 114
Y Y L + + + D++ L DW +
Sbjct: 147 YEYALVDRSGKHDLADLRSLQDWFL 171
>1omo_A Alanine dehydrogenase; two-domain, beta-sandwich-dimer,
rossmann-fold NAD domain, human MU crystallin homolog;
HET: NAD; 2.32A {Archaeoglobus fulgidus} SCOP: c.2.1.13
PDB: 1vll_A
Length = 322
Score = 26.8 bits (60), Expect = 4.0
Identities = 11/24 (45%), Positives = 14/24 (58%)
Query: 125 ECDLEELKRTDPVVDKLYQSTEEG 148
E D+E LK+ VVD L Q+ G
Sbjct: 225 ELDVEILKKAKIVVDDLEQAKHGG 248
>4flb_A Regulation of nuclear PRE-mRNA domain-containing; structural
genomics consortium, SGC, protein binding; 1.80A {Homo
sapiens}
Length = 132
Score = 25.7 bits (56), Expect = 6.2
Identities = 11/60 (18%), Positives = 23/60 (38%), Gaps = 2/60 (3%)
Query: 106 VKDLHDWIVSHFTEHPLFVECDLEELKRTDPV--VDKLYQSTEEGQKVTRNKGEKFCAVF 163
++ L W + + H V ++ L+R+ ++ Y + + Q R F F
Sbjct: 24 IQGLSSWCIENKKHHSTIVYHWMKWLRRSAYPHRLNLFYLANDVIQNCKRKNAIIFRESF 83
>1h6d_A Precursor form of glucose-fructose oxidoreductase; protein
translocation, periplasmic oxidoreductase, signal
peptide, ligand binding,; HET: NDP; 2.05A {Zymomonas
mobilis} SCOP: c.2.1.3 d.81.1.5 PDB: 1h6b_A* 1h6a_A*
1h6c_A* 1ryd_A* 1rye_A* 1ofg_A* 1evj_A*
Length = 433
Score = 25.9 bits (57), Expect = 7.1
Identities = 6/29 (20%), Positives = 13/29 (44%)
Query: 124 VECDLEELKRTDPVVDKLYQSTEEGQKVT 152
V EE + ++ +Y++ G+ V
Sbjct: 394 VRSPGEEGMQDVRLIQAIYEAARTGRPVN 422
>1x6v_B Bifunctional 3'-phosphoadenosine 5'- phosphosulfate synthethase 1;
transferase, ATP sulfurylase, APS kinase, PAPS; HET:
ADP; 1.75A {Homo sapiens} SCOP: b.122.1.3 c.26.1.5
c.37.1.4 PDB: 1xjq_B* 1xnj_B* 2qjf_A* 2ofx_A* 2ofw_A*
Length = 630
Score = 25.9 bits (57), Expect = 8.4
Identities = 18/81 (22%), Positives = 34/81 (41%), Gaps = 16/81 (19%)
Query: 80 RIINQNLLSEYAYVLSEGGIVYTIT-----------DVKDLHDWIVSHFTEHPLFVECDL 128
R N ++E A + ++ G+V IT + + +H+ F E +FV+ L
Sbjct: 106 REENVRRIAEVAKLFADAGLV-CITSFISPYTQDRNNARQIHEGASLPFFE--VFVDAPL 162
Query: 129 EELKRTDPVVDKLYQSTEEGQ 149
++ D LY+ G+
Sbjct: 163 HVCEQRDV--KGLYKKARAGE 181
>2nyk_A M157; LY49, NK cells, viral protein; HET: NAG FUC; 2.10A {Murid
herpesvirus 1}
Length = 285
Score = 25.7 bits (55), Expect = 9.4
Identities = 14/79 (17%), Positives = 26/79 (32%), Gaps = 5/79 (6%)
Query: 3 WSPLYPELKDPTCEKKVEF---VDVGCGKLYLPMFPSTLILGLEIRVKV--SDYVIDEWS 57
W +LK E + + S + +E+ + S V DE +
Sbjct: 164 WRSTVQKLKQLAYMNATEVEFWYNTTGLTTCVVTSRSNVPFTVELSLNTNCSAIVTDEST 223
Query: 58 LYLKKMFFLYPDPHFKRCK 76
+ + + P H +RC
Sbjct: 224 VDCQILTVKAPGSHAQRCY 242
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
0.323 0.142 0.456
Gapped
Lambda K H
0.267 0.0571 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,799,554
Number of extensions: 160546
Number of successful extensions: 385
Number of sequences better than 10.0: 1
Number of HSP's gapped: 378
Number of HSP's successfully gapped: 33
Length of query: 169
Length of database: 6,701,793
Length adjustment: 87
Effective length of query: 82
Effective length of database: 4,272,666
Effective search space: 350358612
Effective search space used: 350358612
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 54 (24.9 bits)