RPS-BLAST 2.2.22 [Sep-27-2009]
Database: pdb70
24,244 sequences; 5,693,230 total letters
Searching..................................................done
Query= gi|254780516|ref|YP_003064929.1| type II modification
methyltransferase [Candidatus Liberibacter asiaticus str. psy62]
(83 letters)
>1g55_A DNA cytosine methyltransferase DNMT2; human DNA methyltransferase
homologue; HET: DNA SAH; 1.80A {Homo sapiens} SCOP:
c.66.1.26
Length = 343
Score = 91.6 bits (226), Expect = 3e-20
Identities = 23/85 (27%), Positives = 46/85 (54%), Gaps = 5/85 (5%)
Query: 2 LKITDLFCGIGGIRLDLEQTFNHRNVECFFSSEINPYSVKTYQANFPNT-LIFGDIAKIK 60
L++ +L+ G+GG+ L ++ + + ++N + + Y+ NFP+T L+ I I
Sbjct: 3 LRVLELYSGVGGMHHALRESC--IPAQVVAAIDVNTVANEVYKYNFPHTQLLAKTIEGIT 60
Query: 61 TQDIP--DHDVLLAGFPCQPFSQAG 83
++ D++L PCQPF++ G
Sbjct: 61 LEEFDRLSFDMILMSPPCQPFTRIG 85
>3me5_A Cytosine-specific methyltransferase; structural genomics, protein
structure initiative, NEW YORK structural genomix
research consortium; 1.75A {Shigella flexneri 2A} PDB:
3lx6_A
Length = 482
Score = 86.8 bits (214), Expect = 1e-18
Identities = 41/101 (40%), Positives = 49/101 (48%), Gaps = 24/101 (23%)
Query: 3 KITDLFCGIGGIRLDLEQTFNHRNVECFFSSEINPYSVKTYQANFPN----TLIFGDIAK 58
+ DLF GIGGIR E +C F+SE N ++V+TY+AN DI
Sbjct: 90 RFIDLFAGIGGIRRGFESI----GGQCVFTSEWNKHAVRTYKANHYCDPATHHFNEDIRD 145
Query: 59 IKTQD----------------IPDHDVLLAGFPCQPFSQAG 83
I IP+HDVLLAGFPCQPFS AG
Sbjct: 146 ITLSHQEGVSDEAAAEHIRQHIPEHDVLLAGFPCQPFSLAG 186
>1dct_A Protein (modification methylase HAEIII); enzyme, cytosine
methylase; HET: DNA C49 5CM; 2.80A {Haemophilus
aegyptus} SCOP: c.66.1.26
Length = 324
Score = 80.8 bits (198), Expect = 6e-17
Identities = 25/79 (31%), Positives = 41/79 (51%), Gaps = 4/79 (5%)
Query: 2 LKITDLFCGIGGIRLDLEQTFNHRNVECFFSSEINPYSVKTYQANFPNTLIFGDIAKIKT 61
+ + LF G GG+ L ++ ++E + KTY++N LI GDI+KI +
Sbjct: 1 MNLISLFSGAGGLDLGFQKA----GFRIICANEYDKSIWKTYESNHSAKLIKGDISKISS 56
Query: 62 QDIPDHDVLLAGFPCQPFS 80
+ P D ++ G PCQ +S
Sbjct: 57 DEFPKCDGIIGGPPCQSWS 75
>2c7p_A Modification methylase HHAI; DNA methyltransferase,
methyltransferase, base flipping, restriction system,
transferase; HET: 5CM A1P SAH EPE CIT; 1.7A
{Haemophilus haemolyticus} SCOP: c.66.1.26 PDB: 10mh_A*
1m0e_A* 1mht_A* 1hmy_A* 1skm_A* 2c7o_A* 2c7q_A* 2hmy_B*
2hr1_A* 3mht_A* 4mht_A* 5mht_A* 6mht_A* 7mht_A* 8mht_A*
9mht_A* 2zcj_A* 2z6u_A* 2z6q_A* 2uz4_A* ...
Length = 327
Score = 79.3 bits (194), Expect = 2e-16
Identities = 37/82 (45%), Positives = 50/82 (60%), Gaps = 5/82 (6%)
Query: 2 LKITDLFCGIGGIRLDLEQTFNHRNVECFFSSEINPYSVKTYQANFPNTLIFGDIAKIKT 61
L+ DLF G+GG RL LE EC +S+E + Y+ + Y+ NF GDI ++
Sbjct: 12 LRFIDLFAGLGGFRLALESC----GAECVYSNEWDKYAQEVYEMNFGEK-PEGDITQVNE 66
Query: 62 QDIPDHDVLLAGFPCQPFSQAG 83
+ IPDHD+L AGFPCQ FS +G
Sbjct: 67 KTIPDHDILCAGFPCQAFSISG 88
>3g7u_A Cytosine-specific methyltransferase; DNA-binding, NAD-binding,
structural genomics, protein structure initiative, PSI;
1.75A {Escherichia coli O157}
Length = 376
Score = 71.3 bits (173), Expect = 5e-14
Identities = 24/89 (26%), Positives = 43/89 (48%), Gaps = 12/89 (13%)
Query: 2 LKITDLFCGIGGIRLDLEQTFNHRNVECFFSSEINPYSVKTYQANFPNTL-IFGDIAKIK 60
L + DLF G+GG+ L + + + EI+ +++ T+ NFP +L + D++ +
Sbjct: 3 LNVIDLFSGVGGLSLGAARA----GFDVKMAVEIDQHAINTHAINFPRSLHVQEDVSLLN 58
Query: 61 TQDIPDH-------DVLLAGFPCQPFSQA 82
+ I D ++ G PCQ FS
Sbjct: 59 AEIIKGFFKNDMPIDGIIGGPPCQGFSSI 87
>2qrv_A DNA (cytosine-5)-methyltransferase 3A; DNA methyltransferase 3A
(DNMT3A) and ITS regulatory factor; HET: DNA SAH; 2.89A
{Homo sapiens}
Length = 295
Score = 66.9 bits (162), Expect = 1e-12
Identities = 18/83 (21%), Positives = 36/83 (43%), Gaps = 6/83 (7%)
Query: 2 LKITDLFCGIGGIRLDLEQTFNHRNVECFFSSEINPYSVKTYQANFPNTLIF-GDIAKIK 60
+++ LF GI L L+ V+ + +SE+ S+ +++ GD+ +
Sbjct: 17 IRVLSLFDGIATGLLVLKDL--GIQVDRYIASEVCEDSITVGMVRHQGKIMYVGDVRSVT 74
Query: 61 ---TQDIPDHDVLLAGFPCQPFS 80
Q+ D+++ G PC S
Sbjct: 75 QKHIQEWGPFDLVIGGSPCNDLS 97
>2qrv_B DNA (cytosine-5)-methyltransferase 3-like; DNA methyltransferase
3A (DNMT3A) and ITS regulatory factor; HET: DNA SAH;
2.89A {Homo sapiens}
Length = 230
Score = 45.3 bits (107), Expect = 3e-06
Identities = 12/82 (14%), Positives = 24/82 (29%), Gaps = 23/82 (28%)
Query: 2 LKITDLFCGIGGIRLDLEQTFNHRNVECFFSSEINPYSVKTYQANFPNTLIFGDIAKIKT 61
+++ LF I L F S +P +K D+
Sbjct: 34 VRVLSLFEDIKKELTSLG----------FLESGSDPGQLKHV----------VDVTDTVR 73
Query: 62 QDIPDH---DVLLAGFPCQPFS 80
+D+ + D++ P +
Sbjct: 74 KDVEEWGPFDLVYGATPPLGHT 95
>2pv0_B DNA (cytosine-5)-methyltransferase 3-like; DNMT3L, unmethylated
H3K4, de novo DNA methylation, transferase regulator;
HET: DNA; 3.30A {Homo sapiens} PDB: 2pvc_B*
Length = 386
Score = 42.6 bits (100), Expect = 2e-05
Identities = 12/82 (14%), Positives = 23/82 (28%), Gaps = 23/82 (28%)
Query: 2 LKITDLFCGIGGIRLDLEQTFNHRNVECFFSSEINPYSVKTYQANFPNTLIFGDIAKIKT 61
+++ LF I L F S +P +K D+
Sbjct: 190 VRVLSLFEDIKKELTSLG----------FLESGSDPGQLKH----------VVDVTDTVR 229
Query: 62 QDI---PDHDVLLAGFPCQPFS 80
+D+ D++ P +
Sbjct: 230 KDVEEWGPFDLVYGATPPLGHT 251
>2ozv_A Hypothetical protein ATU0636; structural genomics, predicted
transferase, predicted O-methyltransferase, PFAM
PF05175, PSI-2; HET: MSE; 1.70A {Agrobacterium
tumefaciens str}
Length = 260
Score = 30.9 bits (69), Expect = 0.066
Identities = 10/81 (12%), Positives = 21/81 (25%), Gaps = 5/81 (6%)
Query: 3 KITDLFCGIGGIRLDLEQTFNHRNVECFFSSEINPYSVKTYQANFPNTLIFGDIAKIK-- 60
+I DL G G + + V + E + + + + A+I+
Sbjct: 39 RIADLGAGAGAAGMAVAARLEKAEVTLY---ERSQEMAEFARRSLELPDNAAFSARIEVL 95
Query: 61 TQDIPDHDVLLAGFPCQPFSQ 81
D+
Sbjct: 96 EADVTLRAKARVEAGLPDEHF 116
>3ll7_A Putative methyltransferase; methytransferase, structural genomics,
MCSG, PSI-2, protein structure initiative; HET: MSE;
1.80A {Porphyromonas gingivalis}
Length = 410
Score = 28.8 bits (64), Expect = 0.33
Identities = 15/65 (23%), Positives = 22/65 (33%), Gaps = 5/65 (7%)
Query: 3 KITDLFCGIGGIRLDLEQTFNHRNVECFFSSEINPYSVKTYQANFPNTLIFGDIAKIKTQ 62
K+ DL G+G + L E N + + N P L G I T
Sbjct: 96 KVVDLTGGLGIDFIAL-----MSKASQGIYIERNDETAVAARHNIPLLLNEGKDVNILTG 150
Query: 63 DIPDH 67
D ++
Sbjct: 151 DFKEY 155
>2ih2_A Modification methylase TAQI; DNA, DNA methyltransferase, target
base partner, 5- methylpyrimidin-2(1H)-ONE, base
flipping; HET: 5PY 6MA NEA; 1.61A {Thermus aquaticus}
SCOP: c.66.1.27 d.287.1.1 PDB: 2ibs_A* 2ibt_A* 2ih4_A*
2ih5_A* 2jg3_A* 2np6_A* 2np7_A* 1aqj_A* 1aqi_A* 2adm_A*
1g38_A*
Length = 421
Score = 26.4 bits (57), Expect = 1.4
Identities = 10/72 (13%), Positives = 21/72 (29%), Gaps = 5/72 (6%)
Query: 3 KITDLFCGIGGIRLDLEQTFNHRNVECFFSSEINPYSVKTYQANFPNTLIFGDIAKIKTQ 62
++ + C G + H F EI+P ++ I D +
Sbjct: 42 RVLEPACAHGPFLRAFRE--AHGTAYRFVGVEIDPKALDLPPW---AEGILADFLLWEPG 96
Query: 63 DIPDHDVLLAGF 74
+ D + +
Sbjct: 97 EAFDLILGNPPY 108
>3gdh_A Trimethylguanosine synthase homolog; M7G, CAP, dimethyltransferase,
usnRNA, snoRNA, telomerase, cytoplasm,
methyltransferase, nucleus; HET: MGP SAH; 2.00A {Homo
sapiens} PDB: 3egi_A*
Length = 241
Score = 25.9 bits (56), Expect = 2.3
Identities = 15/82 (18%), Positives = 24/82 (29%), Gaps = 8/82 (9%)
Query: 3 KITDLFCGIGGIRLDLEQTFNHRNVECFFSSE----INPYSVKTYQANFPNTLIFGDIAK 58
+ D FCG+GG + T V + + + Y I GD
Sbjct: 81 VVVDAFCGVGGNTIQFALTGMR--VIAIDIDPVKIALARNNAEVYGIADKIEFICGDFLL 138
Query: 59 IKTQDIPDHDVLLAGFPCQPFS 80
+ + DV+ P
Sbjct: 139 LASFL--KADVVFLSPPWGGPD 158
>2as0_A Hypothetical protein PH1915; RNA methyltransferase, structural
genomics, PSI, protein structure initiative; 1.80A
{Pyrococcus horikoshii} SCOP: b.122.1.9 c.66.1.51
Length = 396
Score = 25.9 bits (56), Expect = 2.5
Identities = 7/45 (15%), Positives = 18/45 (40%), Gaps = 4/45 (8%)
Query: 3 KITDLFCGIGGIRLDLEQTFNHRNVECFFSSEINPYSVKTYQANF 47
++ D+F GG + + + +P +++T + N
Sbjct: 220 RVLDVFTYTGGFAIHA----AIAGADEVIGIDKSPRAIETAKENA 260
>1ne2_A Hypothetical protein TA1320; structural genomics, conserved
hypothetical protein, PSI, protein structure
initiative; 1.75A {Thermoplasma acidophilum} SCOP:
c.66.1.32
Length = 200
Score = 25.0 bits (54), Expect = 4.5
Identities = 9/47 (19%), Positives = 18/47 (38%), Gaps = 4/47 (8%)
Query: 3 KITDLFCGIGGIRLDLEQTFNHRNVECFFSSEINPYSVKTYQANFPN 49
+ D G G + +V F +I+P +++T + N
Sbjct: 54 SVIDAGTGNGILACGSYL-LGAESVTAF---DIDPDAIETAKRNCGG 96
>3a27_A TYW2, uncharacterized protein MJ1557; wybutosine modification,
transferase; HET: SAM; 2.00A {Methanocaldococcus
jannaschii}
Length = 272
Score = 24.7 bits (53), Expect = 5.4
Identities = 10/39 (25%), Positives = 16/39 (41%), Gaps = 3/39 (7%)
Query: 3 KITDLFCGIGGIRLDLEQTFNHRNVECFFSSEINPYSVK 41
+ D+F GIG + L + + V E NP +
Sbjct: 122 VVVDMFAGIGYFTIPLAKYSKPKLVYAI---EKNPTAYH 157
>1l3i_A Precorrin-6Y methyltransferase/putative decarboxylase; structural
genomics, beta barrel, rossmann fold, tetramer; HET:
SAH; 1.95A {Methanothermobacterthermautotrophicus} SCOP:
c.66.1.22 PDB: 1kxz_A 1l3b_A 1f38_A 1l3c_A*
Length = 192
Score = 24.3 bits (52), Expect = 6.8
Identities = 16/78 (20%), Positives = 30/78 (38%), Gaps = 12/78 (15%)
Query: 3 KITDLFCGIGGIRLDLEQTFNHRNVECFFSSEINPYSVKTYQANFPN-------TLIFGD 55
D+ CG GG+ L+L ++ + NP ++ T + N TL+ GD
Sbjct: 36 VAVDVGCGTGGVTLELAGRVRR-----VYAIDRNPEAISTTEMNLQRHGLGDNVTLMEGD 90
Query: 56 IAKIKTQDIPDHDVLLAG 73
+ + ++ G
Sbjct: 91 APEALCKIPDIDIAVVGG 108
>3lpm_A Putative methyltransferase; structural genomics, protein
structure initiative, NEW YORK structural genomix
research consortium, nysgxrc; 2.40A {Listeria
monocytogenes}
Length = 259
Score = 24.2 bits (52), Expect = 7.4
Identities = 11/45 (24%), Positives = 14/45 (31%), Gaps = 4/45 (8%)
Query: 3 KITDLFCGIGGIRLDLEQTFNHRNVECFFSSEINPYSVKTYQANF 47
KI DL G G I L L + EI + +
Sbjct: 52 KIIDLCSGNGIIPLLLSTRTKAK----IVGVEIQERLADMAKRSV 92
>2yx1_A Hypothetical protein MJ0883; methyl transferase, tRNA modification
enzyme; HET: SFG; 2.20A {Methanocaldococcus jannaschii}
Length = 336
Score = 24.0 bits (51), Expect = 8.1
Identities = 8/39 (20%), Positives = 21/39 (53%), Gaps = 6/39 (15%)
Query: 3 KITDLFCGIGGIRLDLEQTFNHRNVECFFSSEINPYSVK 41
+ D+F G+G + +N + ++ +INP++++
Sbjct: 198 VVVDMFAGVGPFSIA------CKNAKKIYAIDINPHAIE 230
>3jwg_A HEN1, methyltransferase type 12; 1.90A {Clostridium thermocellum}
PDB: 3jwi_A
Length = 219
Score = 23.8 bits (50), Expect = 8.9
Identities = 8/32 (25%), Positives = 13/32 (40%)
Query: 3 KITDLFCGIGGIRLDLEQTFNHRNVECFFSSE 34
K+ DL CG G + L + + + S
Sbjct: 32 KVIDLGCGEGNLLSLLLKDKSFEQITGVDVSY 63
>1eh9_A Glycosyltrehalose trehalohydrolase; alpha/beta barrel, calcium
binding, covalent dimer,; 3.00A {Sulfolobus
solfataricus} SCOP: b.1.18.2 b.71.1.1 c.1.8.1 PDB:
1eha_A
Length = 558
Score = 23.6 bits (50), Expect = 9.6
Identities = 11/43 (25%), Positives = 21/43 (48%)
Query: 13 GIRLDLEQTFNHRNVECFFSSEINPYSVKTYQANFPNTLIFGD 55
G+ + L+ +NH E + ++ PY + Y+ + T F D
Sbjct: 181 GLGVILDVVYNHVGPEGNYMVKLGPYFSQKYKTPWGLTFNFDD 223
Database: pdb70
Posted date: Jan 26, 2011 11:21 AM
Number of letters in database: 5,693,230
Number of sequences in database: 24,244
Lambda K H
0.325 0.143 0.447
Gapped
Lambda K H
0.267 0.0476 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 710,942
Number of extensions: 25506
Number of successful extensions: 96
Number of sequences better than 10.0: 1
Number of HSP's gapped: 86
Number of HSP's successfully gapped: 23
Length of query: 83
Length of database: 5,693,230
Length adjustment: 51
Effective length of query: 32
Effective length of database: 4,456,786
Effective search space: 142617152
Effective search space used: 142617152
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: 50 (23.7 bits)