RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy3543
(250 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 = 196 bits (499), Expect = 1e-61
Identities = 101/245 (41%), Positives = 145/245 (59%), Gaps = 8/245 (3%)
Query: 4 LSNHAFSLEVVTAIDINTSANSVYKHNFPRTNLRGRNIQSFSIEEINAMSPDVILMSPPC 63
L +VV AID+NT AN VYK+NFP T L + I+ ++EE + +S D+ILMSPPC
Sbjct: 19 LRESCIPAQVVAAIDVNTVANEVYKYNFPHTQLLAKTIEGITLEEFDRLSFDMILMSPPC 78
Query: 64 QPFTRTGLQKDIADARCTALSYLIETIPAIPSL-QCLLLENVKGFEGSRSRDLITSMLTR 122
QPFTR G Q D+ D+R + ++++ +P + L + +LLENVKGFE S +RDL+ +
Sbjct: 79 QPFTRIGRQGDMTDSRTNSFLHILDILPRLQKLPKYILLENVKGFEVSSTRDLLIQTIEN 138
Query: 123 AGFRFQEFLLSPTQFGVPNSRTRYYLIAKRSPAAHSSEASFCFETSSELMTELPKLKANT 182
GF++QEFLLSPT G+PNSR RY+LIAK F+ +++ E PK++ +
Sbjct: 139 CGFQYQEFLLSPTSLGIPNSRLRYFLIAKL------QSEPLPFQAPGQVLMEFPKIEIHR 192
Query: 183 CNPLLSRMTLHGILDSTHPSGDLYRRYLVSDKDLLRRFHVFDIVNGKASSTNCFTKAYTH 242
N S +++ + D D+ +YL+ K LLR + DIV + CFTK Y
Sbjct: 193 KNQQDSDLSVKMLKDFLEDDTDVN-QYLLPPKSLLRYALLLDIVQPTCRRSVCFTKGYGS 251
Query: 243 YAEGK 247
Y EG
Sbjct: 252 YIEGT 256
>3qv2_A 5-cytosine DNA methyltransferase; DNMT2, ehmeth; HET: SAH; 2.15A
{Entamoeba histolytica}
Length = 327
Score = 166 bits (421), Expect = 4e-50
Identities = 65/239 (27%), Positives = 105/239 (43%), Gaps = 33/239 (13%)
Query: 12 EVVTAIDINTSANSVYKHNFPRTNLRGRNIQSFSIEEINAMSPDVILMSPPCQPFTR--T 69
DIN AN +Y NF N+ S SI++I +++ + MSPPCQP+
Sbjct: 36 ATFIPFDINEIANKIYSKNFKEEVQVK-NLDSISIKQIESLNCNTWFMSPPCQPYNNSIM 94
Query: 70 GLQKDIADARCTALSYLIETIPAIPSLQ--CLLLENVKGFEGSRSRDLITSMLTRAGFRF 127
KDI D R ++ +L I + + +ENV F+ S I ++L + +
Sbjct: 95 SKHKDINDPRAKSVLHLYRDILPYLINKPKHIFIENVPLFKESLVFKEIYNILIKNQYYI 154
Query: 128 QEFLLSPTQFGVPNSRTRYYLIAKRSPAAHSSEASFCFETSSELMTELPKLKANTCNPLL 187
++ + SP G+PNSRTRYY++A+ +P + E +
Sbjct: 155 KDIICSPIDIGIPNSRTRYYVMARLTP------FKNEIQLHQEKES-------------- 194
Query: 188 SRMTLHGILDSTHPSGDLYRRYLVSDKDLLRRFHVFDIVNGKASSTNCFTKAYTHYAEG 246
+ LD+ ++ Y + +L++ +FDIV T CFTK+YT EG
Sbjct: 195 ---MISNYLDN-----NVNESYSIPSDLILKKGMLFDIVGKDDKRTCCFTKSYTKIVEG 245
>1dct_A Protein (modification methylase HAEIII); enzyme, cytosine
methylase, transferase/DNA complex; HET: DNA C49 5CM;
2.80A {Haemophilus influenzae biotypeaegyptius} SCOP:
c.66.1.26
Length = 324
Score = 94.0 bits (234), Expect = 6e-23
Identities = 36/145 (24%), Positives = 57/145 (39%), Gaps = 9/145 (6%)
Query: 12 EVVTAIDINTSANSVYKHNFPRTNLRGRNIQSFSIEEINAMSPDVILMSPPCQPFTRTGL 71
++ A + + S Y+ N ++G +I S +E D I+ PPCQ ++ G
Sbjct: 23 RIICANEYDKSIWKTYESNHSAKLIKG-DISKISSDEFP--KCDGIIGGPPCQSWSEGGS 79
Query: 72 QKDIADARCTALSYLIETIPAI-PSLQCLLLENVKGF---EGSRSRDLITSMLTRAGFRF 127
+ I D R I + P L ENVKG +++ AG+
Sbjct: 80 LRGIDDPRGKLFYEYIRILKQKKP--IFFLAENVKGMMAQRHNKAVQEFIQEFDNAGYDV 137
Query: 128 QEFLLSPTQFGVPNSRTRYYLIAKR 152
LL+ +GV R R + I R
Sbjct: 138 HIILLNANDYGVAQDRKRVFYIGFR 162
>3g7u_A Cytosine-specific methyltransferase; DNA-binding, NAD-binding,
structural GENO protein structure initiative, PSI; 1.75A
{Escherichia coli O157}
Length = 376
Score = 91.3 bits (227), Expect = 1e-21
Identities = 38/189 (20%), Positives = 70/189 (37%), Gaps = 18/189 (9%)
Query: 12 EVVTAIDINTSANSVYKHNFPRTNLRGRNIQSFSIEEINAMSP-----DVILMSPPCQPF 66
+V A++I+ A + + NFPR+ ++ + E I D I+ PPCQ F
Sbjct: 25 DVKMAVEIDQHAINTHAINFPRSLHVQEDVSLLNAEIIKGFFKNDMPIDGIIGGPPCQGF 84
Query: 67 TRTGLQKDIADARCTALSYLIETIPAI-PSLQCLLLENVKGF---EGSRSRDLITSMLTR 122
+ G + + D+R + + + P L ENV G + S R+ ++++
Sbjct: 85 SSIG-KGNPDDSRNQLYMHFYRLVSELQPLF--FLAENVPGIMQEKYSGIRNKAFNLVSG 141
Query: 123 AGFRFQEFLLSPTQFGVPNSRTRYYLIAKRSPAAHSSEASFCFETSSELMT------ELP 176
+ + +G P RTRY+ I + + +T LP
Sbjct: 142 DYDILDPIKVKASDYGAPTIRTRYFFIGVKKSLKLDISDEVFMPKMIDPVTVKDALYGLP 201
Query: 177 KLKANTCNP 185
+
Sbjct: 202 DIIDANWQS 210
>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*
3eeo_A* 3mht_A* 4mht_A* 5mht_A* 6mht_A* 7mht_A* 8mht_A*
9mht_A* 2zcj_A* 2z6u_A* 2z6q_A* ...
Length = 327
Score = 90.2 bits (224), Expect = 2e-21
Identities = 35/145 (24%), Positives = 64/145 (44%), Gaps = 10/145 (6%)
Query: 12 EVVTAIDINTSANSVYKHNFPRTNLRGRNIQSFSIEEINAMSPDVILMSPPCQPFTRTGL 71
E V + + + A VY+ NF +I + + I D++ PCQ F+ +G
Sbjct: 34 ECVYSNEWDKYAQEVYEMNFGEKPEG--DITQVNEKTIPDH--DILCAGFPCQAFSISGK 89
Query: 72 QKDIADARCTALSYLIETIPAI-PSLQCLLLENVKGFEGS---RSRDLITSMLTRAGFRF 127
QK D+R T + + P + + +ENVK F + +++ + + + F
Sbjct: 90 QKGFEDSRGTLFFDIARIVREKKP--KVVFMENVKNFASHDNGNTLEVVKNTMNELDYSF 147
Query: 128 QEFLLSPTQFGVPNSRTRYYLIAKR 152
+L+ +G+P R R Y+I R
Sbjct: 148 HAKVLNALDYGIPQKRERIYMICFR 172
>3av4_A DNA (cytosine-5)-methyltransferase 1; CXXC-type zinc
finger/C5-methyltransferase family; HET: DNA; 2.75A {Mus
musculus} PDB: 3av5_A* 3av6_A*
Length = 1330
Score = 79.6 bits (195), Expect = 3e-17
Identities = 31/160 (19%), Positives = 58/160 (36%), Gaps = 21/160 (13%)
Query: 12 EVVTAIDINTSANSVYKHNFPRTNLRGRNIQSFSIEEIN-------------AMSPDVIL 58
E + AI++ A ++ N P T + + + +++
Sbjct: 875 ETLWAIEMWDPAAQAFRLNNPGTTVFTEDCNVLLKLVMAGEVTNSLGQRLPQKGDVEMLC 934
Query: 59 MSPPCQPFTRTG--LQKDIADARCTALSYLIETIPAI-PSLQCLLLENVKGF---EGSRS 112
PPCQ F+ + + + + + + P + LLENV+ F S
Sbjct: 935 GGPPCQGFSGMNRFNSRTYSKFKNSLVVSFLSYCDYYRP--RFFLLENVRNFVSYRRSMV 992
Query: 113 RDLITSMLTRAGFRFQEFLLSPTQFGVPNSRTRYYLIAKR 152
L L R G++ +L Q+GV +R R ++A
Sbjct: 993 LKLTLRCLVRMGYQCTFGVLQAGQYGVAQTRRRAIILAAA 1032
>3swr_A DNA (cytosine-5)-methyltransferase 1; epigenetics, DNA
methyltransferase fold, maintenance methyla transferase;
HET: DNA SFG MES; 2.49A {Homo sapiens} PDB: 3pta_A*
3pt6_A* 3pt9_A* 4da4_A*
Length = 1002
Score = 79.5 bits (195), Expect = 4e-17
Identities = 32/163 (19%), Positives = 59/163 (36%), Gaps = 27/163 (16%)
Query: 12 EVVTAIDINTSANSVYKHNFPRTNLRGRNIQSFSIEEIN-------------AMSPDVIL 58
+ + AI++ A ++ N P + + + + +++
Sbjct: 564 DTLWAIEMWDPAAQAFRLNNPGSTVFTEDCNILLKLVMAGETTNSRGQRLPQKGDVEMLC 623
Query: 59 MSPPCQPFTRTG--LQKDIADARCT----ALSYLIETIPAIPSLQCLLLENVKGF---EG 109
PPCQ F+ + + + + LSY P LLENV+ F +
Sbjct: 624 GGPPCQGFSGMNRFNSRTYSKFKNSLVVSFLSYCDYYRPRF-----FLLENVRNFVSFKR 678
Query: 110 SRSRDLITSMLTRAGFRFQEFLLSPTQFGVPNSRTRYYLIAKR 152
S L L R G++ +L Q+GV +R R ++A
Sbjct: 679 SMVLKLTLRCLVRMGYQCTFGVLQAGQYGVAQTRRRAIILAAA 721
>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 = 67.4 bits (164), Expect = 4e-13
Identities = 42/198 (21%), Positives = 69/198 (34%), Gaps = 42/198 (21%)
Query: 12 EVVTAIDINTSANSVYKHNF---PRTNLRGRNIQSFSIEEINAMSP-------------- 54
+ V + N A YK N P T+ +I+ ++ +S
Sbjct: 111 QCVFTSEWNKHAVRTYKANHYCDPATHHFNEDIRDITLSHQEGVSDEAAAEHIRQHIPEH 170
Query: 55 DVILMSPPCQPFTRTGLQKDIA---------DARCTALSYLIETIPAI-PSLQCLLLENV 104
DV+L PCQPF+ G+ K + D + T ++ I A P +LENV
Sbjct: 171 DVLLAGFPCQPFSLAGVSKKNSLGRAHGFACDTQGTLFFDVVRIIDARRP--AMFVLENV 228
Query: 105 KGFEGS---RSRDLITSMLTRAGFRFQEFLLS--------PTQFGVPNSRTRYYLIAKRS 153
K + ++ +I L G+ + + + +P R R L+ R
Sbjct: 229 KNLKSHDKGKTFRIIMQTLDELGYDVADAEDNGPDDPKIIDGKHFLPQHRERIVLVGFRR 288
Query: 154 PAAHSSEASFCFETSSEL 171
+A F SE
Sbjct: 289 DLNL--KADFTLRDISEC 304
>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 = 60.8 bits (147), Expect = 4e-11
Identities = 20/149 (13%), Positives = 45/149 (30%), Gaps = 15/149 (10%)
Query: 9 FSLEVVTAIDINTSANSVYKHNFPRTNLRGRNIQSFSIEEINAMSP-DVILMSPPCQPFT 67
++ A ++ + +V + +++S + + I P D+++ PC +
Sbjct: 38 IQVDRYIASEVCEDSITVGMVRHQGKIMYVGDVRSVTQKHIQEWGPFDLVIGGSPCNDLS 97
Query: 68 RTG-LQKDIADARCTALSYLIETIPAIPSLQC------LLLENVKGFEGSRSRDLITSML 120
+K + + + + L ENV G + I+ L
Sbjct: 98 IVNPARKGLYEGTGRLFFEFYRLLHDARPKEGDDRPFFWLFENVVAM-GVSDKRDISRFL 156
Query: 121 TRAGFRFQEFLLSPTQFGVPNSRTRYYLI 149
+S R RY+
Sbjct: 157 ESNPVMIDAKEVSA-A-----HRARYFWG 179
>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 = 40.2 bits (93), Expect = 5e-04
Identities = 37/281 (13%), Positives = 81/281 (28%), Gaps = 70/281 (24%)
Query: 10 SLEVVTAIDIN-----TSANSVYKHNFPRTNLRGRNIQSFSIEEINAMSPDVILMSPPCQ 64
+ + A +++ T+ R + + + ++A + I +
Sbjct: 255 NAKAWNAFNLSCKILLTT--------------RFKQV----TDFLSAATTTHISLDHHSM 296
Query: 65 PFTRT---GLQKDIADARCTALSYLIETIPAIPSLQCLLLENVKGFEG--SRSRDLITSM 119
T L D R L + T P ++ E+++ + +
Sbjct: 297 TLTPDEVKSLLLKYLDCRPQDLPREVLTT--NPRRLSIIAESIRDGLATWDNWKHVNCDK 354
Query: 120 LTRAGFRFQEFL--LSPTQFGVPNSRTRYYLIAKRSPAAHSSEASFC-------FETSSE 170
LT + L L P ++ R + ++ P+AH
Sbjct: 355 LTTI---IESSLNVLEPAEY-----RKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMV 406
Query: 171 LMTELPKLKANTCNPLLSRMTLHGI-LDSTHPSGDLYR--RYLVSDKDLLRRFHVFDIVN 227
++ +L K P S +++ I L+ + Y R +V ++ + F D++
Sbjct: 407 VVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIP 466
Query: 228 ------------------GKASSTNCFTKAYTHYA--EGKI 248
F + + E KI
Sbjct: 467 PYLDQYFYSHIGHHLKNIEHPERMTLFRMVFLDFRFLEQKI 507
>1i1q_B Anthranilate synthase component II; tryptophan biosynthesis,
lyase; HET: TRP; 1.90A {Salmonella typhimurium} SCOP:
c.23.16.1 PDB: 1i7q_B 1i7s_B*
Length = 192
Score = 34.7 bits (81), Expect = 0.013
Identities = 9/30 (30%), Positives = 14/30 (46%), Gaps = 3/30 (10%)
Query: 39 RN--IQSFSIEEINAMSPDVILMSP-PCQP 65
RN I+ + M V+++SP P P
Sbjct: 31 RNHIPAQTLIDRLATMKNPVLMLSPGPGVP 60
>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 = 35.4 bits (81), Expect = 0.018
Identities = 39/225 (17%), Positives = 57/225 (25%), Gaps = 98/225 (43%)
Query: 31 FPRTNLRGRNIQSFSIEEINAMSPDVILM-SPPCQPFTRTGLQKDIADARCT-------A 82
+P T+L ++ SP M S T+ +Q +
Sbjct: 314 YPNTSLPPSILEDSLENNEGVPSP----MLS--ISNLTQEQVQDYVNKTNSHLPAGKQVE 367
Query: 83 LSYLIETI--------PAIPSLQ--CLLLENVK---GFEGSR----SRDLITSMLTRAGF 125
+S L+ P SL L L K G + SR R L S
Sbjct: 368 IS-LVNGAKNLVVSGPPQ--SLYGLNLTLRKAKAPSGLDQSRIPFSERKLKFSN------ 418
Query: 126 RFQEFLLSPTQFGVPNSRTRYYLIAKRSPAAHSSEASFCFETSSELMTELPKLKANTCNP 185
FL P P + HS
Sbjct: 419 ---RFL--PV--ASP-----F----------HS--------------------------H 430
Query: 186 LLSRMTLHGILDSTHPSGDLYRRYLVSD-KDLLRRFHVFDIVNGK 229
LL I DL + + + KD+ + V+D +G
Sbjct: 431 LLVP-ASDLINK------DLVKNNVSFNAKDI--QIPVYDTFDGS 466
Score = 35.4 bits (81), Expect = 0.019
Identities = 38/248 (15%), Positives = 69/248 (27%), Gaps = 108/248 (43%)
Query: 31 FPRTNLRGRNIQSF--SIEEINAMSP----DVI--------LMSPPCQPFTRTGLQKDIA 76
F L G +I + + + N + ++I + P + + L + +
Sbjct: 91 FENCYLEGNDIHALAAKLLQENDTTLVKTKELIKNYITARIMAKRPFDKKSNSALFRAVG 150
Query: 77 D--ARCTAL--------SYLIETIPAIPSLQCLLLENVKGFEGSRS--RDLITSM----- 119
+ A+ A+ Y E L+ L ++ DLI
Sbjct: 151 EGNAQLVAIFGGQGNTDDYFEE-------LRDL-------YQTYHVLVGDLIKFSAETLS 196
Query: 120 -LTRA----------GFRFQEFLLSPTQFGVPNSRTRYYLIAKRSPAAHSSEASFCFETS 168
L R G E+L +P+ P+ YL+ S S
Sbjct: 197 ELIRTTLDAEKVFTQGLNILEWLENPSN--TPDK---DYLL--------SIPISC----- 238
Query: 169 SELMTELPKLKANTCNPLLSRMTLHGILDSTHPSGDLYRRYLVSDKDL-LRRFHVFDIVN 227
PL+ G++ H Y+V+ K L + +
Sbjct: 239 ----------------PLI------GVIQLAH--------YVVTAKLLGFTPGELRSYLK 268
Query: 228 GKASSTNC 235
G +T
Sbjct: 269 G---ATGH 273
Score = 32.3 bits (73), Expect = 0.15
Identities = 23/126 (18%), Positives = 44/126 (34%), Gaps = 35/126 (27%)
Query: 8 AFSLEVVTAIDI-----NTSANSVYKHNFPRTNLR------GRNIQSFS-------IEEI 49
S+E + +++ T +V + R+N GR SFS +E +
Sbjct: 1776 VMSIE--SLVEVVFYRGMTMQVAVPRDELGRSNYGMIAINPGRVAASFSQEALQYVVERV 1833
Query: 50 NAMSPDVILMSPPCQP--FTRTGLQKDIA------DARCTALSYL-IETIPAIPSLQCLL 100
+ + + + Q A D L+++ ++ I I + L
Sbjct: 1834 GKRTGWL------VEIVNYNVENQQYVAAGDLRALDTVTNVLNFIKLQKIDIIELQKSLS 1887
Query: 101 LENVKG 106
LE V+G
Sbjct: 1888 LEEVEG 1893
Score = 28.9 bits (64), Expect = 2.0
Identities = 40/252 (15%), Positives = 76/252 (30%), Gaps = 91/252 (36%)
Query: 73 KDIADARCTALSYLIETIPAIPSLQCLLLENVKG----FEGSRSRDL------------- 115
+D+ + A ++ +T S+ +++ N F G + + +
Sbjct: 1643 QDVWNR---ADNHFKDTYGF--SILDIVINNPVNLTIHFGGEKGKRIRENYSAMIFETIV 1697
Query: 116 ------------ITSMLTRAGFRFQEFLLSPTQFGVP----NSRTRYYLIAKR----SPA 155
I T FR ++ LLS TQF P + + + + + A
Sbjct: 1698 DGKLKTEKIFKEINEHSTSYTFRSEKGLLSATQFTQPALTLMEKAAFEDLKSKGLIPADA 1757
Query: 156 A---HS--------SEA-SFCFETSSEL--------MTELPKLKANT-------CNPLLS 188
HS S A E+ E+ +P+ + NP
Sbjct: 1758 TFAGHSLGEYAALASLADVMSIESLVEVVFYRGMTMQVAVPRDELGRSNYGMIAINP--G 1815
Query: 189 RMTLHGILDSTHPSGDLYRRYLVSDKDLLRRFHVFDIVN-----------GKASSTNCFT 237
R+ ++ +Y+V ++ R + +IVN G + + T
Sbjct: 1816 RVAASFSQEAL--------QYVV-ERVGKRTGWLVEIVNYNVENQQYVAAGDLRALDTVT 1866
Query: 238 KAYTHYAEGKID 249
KID
Sbjct: 1867 NVLNFIKLQKID 1878
>1qdl_B Protein (anthranilate synthase (TRPG-SUBUNIT)); tryptophan
biosynthesis, glutamine amidotransferase, allosteric
interaction, lyase; 2.50A {Sulfolobus solfataricus}
SCOP: c.23.16.1
Length = 195
Score = 32.8 bits (76), Expect = 0.058
Identities = 9/22 (40%), Positives = 14/22 (63%), Gaps = 1/22 (4%)
Query: 45 SIEEINAMSPDVILMSP-PCQP 65
SI+ I + PD +++SP P P
Sbjct: 37 SIKGIERIDPDRLIISPGPGTP 58
>3dmg_A Probable ribosomal RNA small subunit methyltransf;
monomethyltranserase, 16S rRNA methyltransferase, N2
G1207 methyltransferase; HET: SAH; 1.55A {Thermus
thermophilus} PDB: 3dmf_A* 3dmh_A* 2zul_A* 2zwv_A*
Length = 381
Score = 32.6 bits (74), Expect = 0.10
Identities = 8/50 (16%), Positives = 21/50 (42%), Gaps = 1/50 (2%)
Query: 14 VTAIDINTSANSVYKHNFPRTNLRGRNIQSFSIEEINA-MSPDVILMSPP 62
V ++ + ++ + L+ + + S E + D+I+ +PP
Sbjct: 258 VVGVEDDLASVLSLQKGLEANALKAQALHSDVDEALTEEARFDIIVTNPP 307
>2p65_A Hypothetical protein PF08_0063; CLPB, malaria, structural genomics,
structural genomics consortium, SGC, unknown function;
1.70A {Plasmodium falciparum}
Length = 187
Score = 31.2 bits (71), Expect = 0.17
Identities = 15/41 (36%), Positives = 21/41 (51%), Gaps = 3/41 (7%)
Query: 180 ANTCNPLLSRMTLHGILDSTHPSGDLYRRYLVSDKDLLRRF 220
N P+L+R L I +T YR+++ DK L RRF
Sbjct: 141 GNILKPMLARGELRCIGATTV---SEYRQFIEKDKALERRF 178
>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 = 31.5 bits (72), Expect = 0.18
Identities = 15/52 (28%), Positives = 21/52 (40%), Gaps = 3/52 (5%)
Query: 14 VTAIDINTSANSVYKHNFPRTNLRGRNI---QSFSIEEINAMSPDVILMSPP 62
T DIN A + K N NL +I S E + + I+ +PP
Sbjct: 77 TTMADINRRAIKLAKENIKLNNLDNYDIRVVHSDLYENVKDRKYNKIITNPP 128
>3ll7_A Putative methyltransferase; methytransferase, structural genomics,
MCSG, PSI-2, protein initiative; HET: MSE; 1.80A
{Porphyromonas gingivalis}
Length = 410
Score = 31.7 bits (71), Expect = 0.24
Identities = 11/55 (20%), Positives = 19/55 (34%), Gaps = 6/55 (10%)
Query: 14 VTAIDINTSANSVYKHNFPRTNLRGRNIQSFS------IEEINAMSPDVILMSPP 62
I+ N +HN P G+++ + + I PD I + P
Sbjct: 118 GIYIERNDETAVAARHNIPLLLNEGKDVNILTGDFKEYLPLIKTFHPDYIYVDPA 172
>1jbk_A CLPB protein; beta barrel, chaperone; 1.80A {Escherichia coli}
SCOP: c.37.1.20
Length = 195
Score = 30.8 bits (70), Expect = 0.27
Identities = 16/41 (39%), Positives = 21/41 (51%), Gaps = 3/41 (7%)
Query: 180 ANTCNPLLSRMTLHGILDSTHPSGDLYRRYLVSDKDLLRRF 220
N P L+R LH + +T D YR+Y+ D L RRF
Sbjct: 140 GNMLKPALARGELHCVGATTL---DEYRQYIEKDAALERRF 177
>2x4l_A Ferric-siderophore receptor protein; transport; 1.50A {Streptomyces
coelicolor}
Length = 325
Score = 30.7 bits (69), Expect = 0.45
Identities = 6/40 (15%), Positives = 19/40 (47%)
Query: 38 GRNIQSFSIEEINAMSPDVILMSPPCQPFTRTGLQKDIAD 77
G ++E+ +++P+V++ + T + ++ D
Sbjct: 95 GNEWGKLNVEKYASLAPEVLITTTFDTAGTLWSVPEESKD 134
>3q87_B N6 adenine specific DNA methylase; SAM-methyltransferase,
methyltransferase, methylation, trans
activator-transferase complex; HET: SAM; 2.00A
{Encephalitozoon cuniculi}
Length = 170
Score = 29.4 bits (66), Expect = 0.69
Identities = 11/59 (18%), Positives = 24/59 (40%), Gaps = 8/59 (13%)
Query: 4 LSNHAFSLEVVTAIDINTSANSVYKHNFPRTNLRGRNIQSFSIEEINAMSPDVILMSPP 62
++ V + D+N A ++ +++ + IN S DV++ +PP
Sbjct: 37 ITEQLRKRNTVVSTDLNIRALESHRGGNL--------VRADLLCSINQESVDVVVFNPP 87
>4dcm_A Ribosomal RNA large subunit methyltransferase G; 23S rRNA
(guanine1835-N2)-methyltransferase; HET: SAM; 2.30A
{Escherichia coli}
Length = 375
Score = 29.9 bits (67), Expect = 0.73
Identities = 7/53 (13%), Positives = 20/53 (37%), Gaps = 4/53 (7%)
Query: 14 VTAIDINTSANSVYKHNFPRTNLRGRN----IQSFSIEEINAMSPDVILMSPP 62
V +D + A + + N + + + ++ + + +L +PP
Sbjct: 249 VVFVDESPMAVASSRLNVETNMPEALDRCEFMINNALSGVEPFRFNAVLCNPP 301
>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 = 29.7 bits (66), Expect = 0.74
Identities = 12/115 (10%), Positives = 26/115 (22%), Gaps = 21/115 (18%)
Query: 39 RNIQSFSIEEINAMSPDVILMSPPCQPFTRTGLQKDIADARCTALSYLIETI------PA 92
+ +EE D++ + P T L + P
Sbjct: 69 TDTVRKDVEEWGPF--DLVYGATPPLGHT-------CDRPPSWYLFQFHRLLQYARPKPG 119
Query: 93 IPSLQCLLLENVKGFEGSRSRDLITSMLTRAGFRFQEFLLSPTQFGVPNSRTRYY 147
P + + D+ + L + + G + R +
Sbjct: 120 SPRPFFWMFVDNLVL-NKEDLDVASRFL-----EMEPVTIPDVHGGSLQNAVRVW 168
>2r79_A Periplasmic binding protein; heme transport, transport prote; HET:
HEM; 2.40A {Pseudomonas aeruginosa}
Length = 283
Score = 29.6 bits (67), Expect = 0.76
Identities = 6/29 (20%), Positives = 15/29 (51%), Gaps = 6/29 (20%)
Query: 38 GRNIQSF------SIEEINAMSPDVILMS 60
RN+ + S+E + A+ P ++++
Sbjct: 173 ARNLATHEGYKPISVEALAALDPVAVVIA 201
>2chu_A CEUE, enterochelin uptake periplasmic binding protein; iron, mecam,
SELF assembly, siderophore; HET: ECA; 2.40A
{Campylobacter jejuni} SCOP: c.92.2.4
Length = 296
Score = 29.7 bits (67), Expect = 0.92
Identities = 15/57 (26%), Positives = 25/57 (43%), Gaps = 6/57 (10%)
Query: 10 SLEVVTAIDINTSANSVYKHNFP--RTNLRGR----NIQSFSIEEINAMSPDVILMS 60
L+ A+ +N V N P + + +Q E INA+ PD+I++S
Sbjct: 46 ILDTFDALKLNDKVVGVPAKNLPKYLQQFKNKPSVGGVQQVDFEAINALKPDLIIIS 102
>2etv_A Iron(III) ABC transporter, periplasmic iron-bindi protein,
putative; periplasmic iron-binding protein, structural
genomics; HET: MLY; 1.70A {Thermotoga maritima} SCOP:
c.92.2.4
Length = 346
Score = 29.3 bits (65), Expect = 1.3
Identities = 8/52 (15%), Positives = 17/52 (32%), Gaps = 5/52 (9%)
Query: 14 VTAIDINTSANSVYKHNFPR-----TNLRGRNIQSFSIEEINAMSPDVILMS 60
V + Y +P + G +E + + PDV+ ++
Sbjct: 52 VEDFEXLRPYGRPYILAYPELXXLPSVGPGGPGXLPDLESLITLQPDVVFIT 103
>2r7a_A Bacterial heme binding protein; periplasmic binding protein, heme
transport, transport protein; HET: HEM; 2.05A {Shigella
dysenteriae} PDB: 2rg7_A
Length = 256
Score = 28.7 bits (65), Expect = 1.4
Identities = 7/29 (24%), Positives = 15/29 (51%), Gaps = 6/29 (20%)
Query: 38 GRNIQSF------SIEEINAMSPDVILMS 60
N+ + S E + A +P+VI+++
Sbjct: 171 AENVATHQQYKSYSAESLIAANPEVIVVT 199
>3tef_A VCTP, iron(III) ABC transporter, periplasmic iron-compo binding
protein; siderophore-binding protein, transport
protein; 1.70A {Vibrio cholerae}
Length = 292
Score = 28.9 bits (65), Expect = 1.4
Identities = 5/16 (31%), Positives = 8/16 (50%)
Query: 45 SIEEINAMSPDVILMS 60
E I PD+I++
Sbjct: 71 DFETIYTQKPDLIVIG 86
>3psh_A Protein HI_1472; substrate binding protein, periplasmic binding
protein, MOLY binding protein, metal transport; 1.50A
{Haemophilus influenzae} PDB: 3psa_A
Length = 326
Score = 28.9 bits (65), Expect = 1.6
Identities = 7/21 (33%), Positives = 15/21 (71%)
Query: 40 NIQSFSIEEINAMSPDVILMS 60
++ S +IE + A+ PDV+ ++
Sbjct: 71 DLNSVNIESLLALKPDVVFVT 91
>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 = 28.4 bits (63), Expect = 1.8
Identities = 14/49 (28%), Positives = 20/49 (40%), Gaps = 6/49 (12%)
Query: 14 VTAIDINTSANSVYKHNFPRTNLRGRNIQSFSIEEINAMSPDVILMSPP 62
VTA DI+ A K N N ++ S + D +M+PP
Sbjct: 77 VTAFDIDPDAIETAKRNCGGVNFMVADVSEISGK------YDTWIMNPP 119
>2q8p_A Iron-regulated surface determinant E; helical backbone metal
receptor superfamily, metal transport; HET: HEM; 1.95A
{Staphylococcus aureus subsp} PDB: 2q8q_A*
Length = 260
Score = 28.5 bits (64), Expect = 1.8
Identities = 3/34 (8%), Positives = 12/34 (35%)
Query: 40 NIQSFSIEEINAMSPDVILMSPPCQPFTRTGLQK 73
++E + + P +L + + ++
Sbjct: 47 QPMEPNVEAVKKLKPTHVLSVSTIKDEMQPFYKQ 80
Score = 26.9 bits (60), Expect = 5.6
Identities = 9/32 (28%), Positives = 15/32 (46%), Gaps = 8/32 (25%)
Query: 38 GRNI--------QSFSIEEINAMSPDVILMSP 61
G N+ S + E + ++PD+IL P
Sbjct: 168 GENVIKVKDRQYISSNTENLLNINPDIILRLP 199
>3mwf_A Iron-regulated ABC transporter siderophore-bindin SIRA; ABC
transporter binding protein, transport protein; HET:
SE8; 1.70A {Staphylococcus aureus subsp} PDB: 3mwg_A
Length = 298
Score = 28.6 bits (64), Expect = 2.2
Identities = 7/17 (41%), Positives = 13/17 (76%)
Query: 45 SIEEINAMSPDVILMSP 61
++EEI+ + PD+I+ S
Sbjct: 75 NLEEISKLKPDLIVASK 91
>3gfv_A Uncharacterized ABC transporter solute-binding protein YCLQ;
alpha-beta-sandwich, periplasmic binding protein fold
(PBP fold); 1.75A {Bacillus subtilis subsp}
Length = 303
Score = 28.2 bits (63), Expect = 2.8
Identities = 4/16 (25%), Positives = 11/16 (68%)
Query: 45 SIEEINAMSPDVILMS 60
+++ + PD+I++S
Sbjct: 87 DFDKVAELDPDLIIIS 102
>1efd_N Ferrichrome-binding periplasmic protein; periplasmic binding
protein-siderophore complex, FHUD complex with
gallichrome; HET: GCR; 1.90A {Escherichia coli} SCOP:
c.92.2.1 PDB: 1k7s_N* 1k2v_N* 1esz_A*
Length = 266
Score = 27.8 bits (62), Expect = 2.9
Identities = 4/17 (23%), Positives = 9/17 (52%)
Query: 45 SIEEINAMSPDVILMSP 61
++E + M P ++ S
Sbjct: 58 NLELLTEMKPSFMVWSA 74
>3be6_A Putative iron compound-binding protein of ABC TRA family; open
form, closed form, group III periplasmic binding protei
structural genomics; HET: MSE; 1.82A {Escherichia coli
O157} PDB: 3be5_A*
Length = 297
Score = 27.9 bits (62), Expect = 2.9
Identities = 8/17 (47%), Positives = 10/17 (58%)
Query: 45 SIEEINAMSPDVILMSP 61
IE I A PD+I+ P
Sbjct: 82 DIEAIVAAKPDLIITEP 98
>3lhs_A Ferrichrome ABC transporter lipoprotein; siderophore, iron,
receptor, binding protein, T protein; HET: SF8; 1.30A
{Staphylococcus aureus subsp} PDB: 3eiw_A 3eix_A*
3li2_A*
Length = 296
Score = 27.8 bits (62), Expect = 2.9
Identities = 8/34 (23%), Positives = 15/34 (44%), Gaps = 8/34 (23%)
Query: 45 SIEEINAMSPDVILMSPPCQPFTRTGLQKDIADA 78
++EEI+ + PD+I+ + K I
Sbjct: 77 NLEEISKLKPDLIIAD--------SSRHKGINKE 102
>4dmg_A Putative uncharacterized protein TTHA1493; rRNA, methyltransferase,
S-adenosyl-methionine, 23S ribosoma transferase; HET:
SAM; 1.70A {Thermus thermophilus}
Length = 393
Score = 28.0 bits (63), Expect = 3.0
Identities = 10/68 (14%), Positives = 23/68 (33%), Gaps = 6/68 (8%)
Query: 14 VTAIDINTSANSVYKHNFPRTNLRGRNIQSFSIEEINAMSP--DVILMSPPCQPFTRTGL 71
A+D + A V R LR ++ + + +L+ PP +
Sbjct: 239 ALAVDKDLEALGVLDQAALRLGLRVDIRHGEALPTLRGLEGPFHHVLLDPP--TLVKR-- 294
Query: 72 QKDIADAR 79
+++ +
Sbjct: 295 PEELPAMK 302
>3g9q_A Ferrichrome-binding protein; alpha-beta protein, structural
genomics, PSI-2, protein STRU initiative; 2.60A
{Bacillus subtilis subsp} PDB: 3hxp_A
Length = 279
Score = 27.7 bits (62), Expect = 3.0
Identities = 5/16 (31%), Positives = 13/16 (81%)
Query: 45 SIEEINAMSPDVILMS 60
S+E++ ++PD+I++
Sbjct: 63 SVEKVIDLNPDLIIVW 78
>2wi8_A Iron-uptake system-binding protein; bacillibactin and enterobactin
binding, triscatecholate BIND protein, iron transport;
1.55A {Bacillus subtilis} PDB: 2why_A 2xuz_A* 2xv1_A*
2phz_A
Length = 311
Score = 27.8 bits (62), Expect = 3.4
Identities = 10/16 (62%), Positives = 12/16 (75%)
Query: 45 SIEEINAMSPDVILMS 60
+IE+I M PDVIL S
Sbjct: 88 NIEKILEMKPDVILAS 103
>3md9_A Hemin-binding periplasmic protein HMUT; transport protein, alpha
beta protein, rigid helical backbon substrate-free, heme
transport; 1.50A {Yersinia pestis} PDB: 3nu1_A*
Length = 255
Score = 27.6 bits (62), Expect = 3.4
Identities = 8/30 (26%), Positives = 15/30 (50%), Gaps = 7/30 (23%)
Query: 38 GRNI-------QSFSIEEINAMSPDVILMS 60
G N + S E + A +PD++L++
Sbjct: 166 GSNAMQGFSRYRPLSQEGVIASAPDLLLIT 195
>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 = 27.3 bits (60), Expect = 5.0
Identities = 12/51 (23%), Positives = 24/51 (47%), Gaps = 2/51 (3%)
Query: 14 VTAIDINTSANSVYKHNFPRTNLRGRN--IQSFSIEEINAMSPDVILMSPP 62
V AIDI+ ++ ++N + + I + + + DV+ +SPP
Sbjct: 103 VIAIDIDPVKIALARNNAEVYGIADKIEFICGDFLLLASFLKADVVFLSPP 153
>3r5t_A Ferric vibriobactin ABC transporter, periplasmic
vibriobactin-binding protein; iron-vibriobactin
transport protein; HET: VBN; 1.45A {Vibrio cholerae}
PDB: 3r5s_A*
Length = 305
Score = 27.1 bits (60), Expect = 5.3
Identities = 6/22 (27%), Positives = 11/22 (50%)
Query: 40 NIQSFSIEEINAMSPDVILMSP 61
S +E + PD+I++S
Sbjct: 73 PAGSVDLESVYVEQPDLIVVSM 94
>1wy7_A Hypothetical protein PH1948; seven-stranded beta sheet,
methyltransferase fold, structura genomics, transferase;
HET: SAH; 2.20A {Pyrococcus horikoshii} SCOP: c.66.1.32
Length = 207
Score = 26.6 bits (58), Expect = 6.8
Identities = 12/78 (15%), Positives = 27/78 (34%), Gaps = 3/78 (3%)
Query: 14 VTAIDINTSANSVYKHNFPRTNLRGRNIQSFSIEEINAMSPDVILMSPPCQPFTRTGLQK 73
V ++++ A V N + + E D+++M+PP + +
Sbjct: 75 VICVEVDKEAVDVLIENLGEFKGKFKVFIGDVSE--FNSRVDIVIMNPPFGSQRKHADRP 132
Query: 74 DIADA-RCTALSYLIETI 90
+ A + + Y I
Sbjct: 133 FLLKAFEISDVVYSIHLA 150
>1r6b_X CLPA protein; AAA+, N-terminal domain, CLPS, crystal, binding
mechanism, hydrolase; HET: ADP; 2.25A {Escherichia coli}
SCOP: a.174.1.1 c.37.1.20 c.37.1.20 PDB: 1ksf_X*
Length = 758
Score = 26.8 bits (60), Expect = 7.5
Identities = 15/46 (32%), Positives = 20/46 (43%), Gaps = 3/46 (6%)
Query: 180 ANTCNPLLSRMTLHGILDSTHPSGDLYRRYLVSDKDLLRRFHVFDI 225
AN PLLS + I +T+ + D+ L RRF DI
Sbjct: 304 ANLIKPLLSSGKIRVIGSTTY---QEFSNIFEKDRALARRFQKIDI 346
>1n2z_A Vitamin B12 transport protein BTUF; HET: CNC PG4; 2.00A
{Escherichia coli} SCOP: c.92.2.2 PDB: 2qi9_F* 4dbl_E
1n4a_A* 1n4d_A
Length = 245
Score = 26.5 bits (59), Expect = 8.0
Identities = 9/31 (29%), Positives = 14/31 (45%), Gaps = 8/31 (25%)
Query: 38 GRNI--------QSFSIEEINAMSPDVILMS 60
G NI S E++ A SP I+++
Sbjct: 164 GENIFKDSRVPWPQVSREQVLARSPQAIVIT 194
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
0.321 0.133 0.389
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: 3,673,204
Number of extensions: 204933
Number of successful extensions: 443
Number of sequences better than 10.0: 1
Number of HSP's gapped: 415
Number of HSP's successfully gapped: 56
Length of query: 250
Length of database: 6,701,793
Length adjustment: 91
Effective length of query: 159
Effective length of database: 4,160,982
Effective search space: 661596138
Effective search space used: 661596138
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 56 (25.4 bits)