BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= 046469
(521 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4FT2|A Chain A, Crystal Structure Of Zea Mays Zmet2 In Complex
H3(1-15)k9me2 Peptide And Sah
pdb|4FT2|B Chain B, Crystal Structure Of Zea Mays Zmet2 In Complex
H3(1-15)k9me2 Peptide And Sah
pdb|4FT4|B Chain B, Crystal Structure Of Zea Mays Zmet2 In Complex
H3(1-32)k9me2 Peptide And Sah
pdb|4FT4|A Chain A, Crystal Structure Of Zea Mays Zmet2 In Complex
H3(1-32)k9me2 Peptide And Sah
Length = 784
Score = 429 bits (1103), Expect = e-120, Method: Compositional matrix adjust.
Identities = 234/501 (46%), Positives = 302/501 (60%), Gaps = 69/501 (13%)
Query: 30 DDEDKIVSNVECHYAQARIGECIFDLGDCAYIK-GEGTQKHIGKILEFFKTTDGEEYFRV 88
D+E+++ CHY A++ ++ LGD Y+K GE +IG+I EFF+ TD YF
Sbjct: 37 DEEEEL--KARCHYRSAKVDNVVYCLGDDVYVKAGENEADYIGRITEFFEGTDQCHYFTC 94
Query: 89 QWFYRAEDTVMKEAADF------HDRKRLFYSTVMNDNPVDCIISKVIVAQIPPKIGLKS 142
+WF+RAEDTV+ HD +R+F S NDN +DCIISKV + + P + K+
Sbjct: 95 RWFFRAEDTVINSLVSISVDGHKHDPRRVFLSEEKNDNVLDCIISKVKIVHVDPNMDPKA 154
Query: 143 NS--IPSSDFYFDMEYCVEYSTFRTLLTGKIHDLSLPSCTETVPTTATSTFFENMPNHGP 200
+ I S D Y+DM Y V YSTF I + S ++T ++ + P
Sbjct: 155 KAQLIESCDLYYDMSYSVAYSTF-----ANISSENGQSGSDTASGISSDDVDLETSSSMP 209
Query: 201 HKAELALLDLYSGCGGMSTGLCLGAKLSCTNLVTRWALDSDKSACESLKLNHPEAQVRNE 260
+ LLDLYSGCGGMSTGLCLGA LS L TRWA+D + AC+SLK NHP+ +VRNE
Sbjct: 210 TRTA-TLLDLYSGCGGMSTGLCLGAALSGLKLETRWAVDFNSFACQSLKYNHPQTEVRNE 268
Query: 261 AAEDFLELVKEWQKLCKRFAVNIVERENKQRSMSQRVTRNSVNSPSITRNSVDSPKVTGN 320
A++FL L+KEW LCK++ Q V N +S + D
Sbjct: 269 KADEFLALLKEWAVLCKKYV--------------QDVDSNLASS----EDQADE------ 304
Query: 321 SVDSPRVTRSSVNSPRVTRNSVNSPRDVDIPPGEYEVARIVDICYGDPNESGKRGLNFKV 380
+SP D D E+ V ++V ICYG + + G+ FKV
Sbjct: 305 ----------------------DSPLDKD----EFVVEKLVGICYGGSDR--ENGIYFKV 336
Query: 381 HWKGYSTSEDSWEPIEGLRNCPERIKEFVRNGFKSKILPLPGDVDVICGGPPCQGISGYN 440
W+GY ED+WEPI+ L +CP++I+EFV+ G K KILPLPGDVDVICGGPPCQGISG+N
Sbjct: 337 QWEGYGPEEDTWEPIDNLSDCPQKIREFVQEGHKRKILPLPGDVDVICGGPPCQGISGFN 396
Query: 441 RFRNVDSPLDDERNRQIVIFMDIVEFLKPKYVLMENVVDILKFDKASLGRYALSRLVHMK 500
R+RN D PL DE+N+Q+V FMDIV +LKPKYVLMENVVDILKF LG+YALS LV MK
Sbjct: 397 RYRNRDEPLKDEKNKQMVTFMDIVAYLKPKYVLMENVVDILKFADGYLGKYALSCLVAMK 456
Query: 501 YQARFGIIAAGCYGLPQFRLR 521
YQAR G++ AGCYGLPQFR+R
Sbjct: 457 YQARLGMMVAGCYGLPQFRMR 477
>pdb|4FSX|A Chain A, Crystal Structure Of Se-Substituted Zea Mays Zmet2 In
Complex With Sah
pdb|4FSX|B Chain B, Crystal Structure Of Se-Substituted Zea Mays Zmet2 In
Complex With Sah
Length = 784
Score = 410 bits (1054), Expect = e-115, Method: Compositional matrix adjust.
Identities = 229/501 (45%), Positives = 292/501 (58%), Gaps = 69/501 (13%)
Query: 30 DDEDKIVSNVECHYAQARIGECIFDLGDCAYIK-GEGTQKHIGKILEFFKTTDGEEYFRV 88
D+E+++ CHY A++ ++ LGD Y+K GE +IG+I EFF+ TD YF
Sbjct: 37 DEEEEL--KARCHYRSAKVDNVVYCLGDDVYVKAGENEADYIGRITEFFEGTDQCHYFTC 94
Query: 89 QWFYRAEDTVMKEAADF------HDRKRLFYSTVMNDNPVDCIISKVIVAQIPPKIGLKS 142
+WF+RAEDTV+ HD +R+F S NDN +DCIISKV + + P K+
Sbjct: 95 RWFFRAEDTVINSLVSISVDGHKHDPRRVFLSEEKNDNVLDCIISKVKIVHVDPNXDPKA 154
Query: 143 NS--IPSSDFYFDMEYCVEYSTFRTLLTGKIHDLSLPSCTETVPTTATSTFFENMPNHGP 200
+ I S D Y+D Y V YSTF I + S ++T ++ + P
Sbjct: 155 KAQLIESCDLYYDXSYSVAYSTF-----ANISSENGQSGSDTASGISSDDVDLETSSSXP 209
Query: 201 HKAELALLDLYSGCGGMSTGLCLGAKLSCTNLVTRWALDSDKSACESLKLNHPEAQVRNE 260
+ LLDLYSGCGG STGLCLGA LS L TRWA+D + AC+SLK NHP+ +VRNE
Sbjct: 210 TRT-ATLLDLYSGCGGXSTGLCLGAALSGLKLETRWAVDFNSFACQSLKYNHPQTEVRNE 268
Query: 261 AAEDFLELVKEWQKLCKRFAVNIVERENKQRSMSQRVTRNSVNSPSITRNSVDSPKVTGN 320
A++FL L+KEW LCK++ Q V N +S + D
Sbjct: 269 KADEFLALLKEWAVLCKKYV--------------QDVDSNLASS----EDQADE------ 304
Query: 321 SVDSPRVTRSSVNSPRVTRNSVNSPRDVDIPPGEYEVARIVDICYGDPNESGKRGLNFKV 380
+SP D D E+ V ++V ICYG + + G+ FKV
Sbjct: 305 ----------------------DSPLDKD----EFVVEKLVGICYGGSDR--ENGIYFKV 336
Query: 381 HWKGYSTSEDSWEPIEGLRNCPERIKEFVRNGFKSKILPLPGDVDVICGGPPCQGISGYN 440
W+GY ED+WEPI+ L +CP++I+EFV+ G K KILPLPGDVDVICGGPPCQGISG+N
Sbjct: 337 QWEGYGPEEDTWEPIDNLSDCPQKIREFVQEGHKRKILPLPGDVDVICGGPPCQGISGFN 396
Query: 441 RFRNVDSPLDDERNRQIVIFMDIVEFLKPKYVLMENVVDILKFDKASLGRYALSRLVHMK 500
R+RN D PL DE+N+Q V F DIV +LKPKYVL ENVVDILKF LG+YALS LV K
Sbjct: 397 RYRNRDEPLKDEKNKQXVTFXDIVAYLKPKYVLXENVVDILKFADGYLGKYALSCLVAXK 456
Query: 501 YQARFGIIAAGCYGLPQFRLR 521
YQAR G AGCYGLPQFR R
Sbjct: 457 YQARLGXXVAGCYGLPQFRXR 477
>pdb|3SWR|A Chain A, Structure Of Human Dnmt1 (601-1600) In Complex With
Sinefungin
Length = 1002
Score = 90.9 bits (224), Expect = 1e-18, Method: Compositional matrix adjust.
Identities = 42/108 (38%), Positives = 66/108 (61%), Gaps = 2/108 (1%)
Query: 414 KSKILPLPGDVDVICGGPPCQGISGYNRFRNVDSPLDDERNRQIVIFMDIVEFLKPKYVL 473
+ + LP GDV+++CGGPPCQG SG NRF + +N +V F+ ++ +P++ L
Sbjct: 609 RGQRLPQKGDVEMLCGGPPCQGFSGMNRFNS--RTYSKFKNSLVVSFLSYCDYYRPRFFL 666
Query: 474 MENVVDILKFDKASLGRYALSRLVHMKYQARFGIIAAGCYGLPQFRLR 521
+ENV + + F ++ + + L LV M YQ FG++ AG YG+ Q R R
Sbjct: 667 LENVRNFVSFKRSMVLKLTLRCLVRMGYQCTFGVLQAGQYGVAQTRRR 714
Score = 43.5 bits (101), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 59/226 (26%), Positives = 88/226 (38%), Gaps = 22/226 (9%)
Query: 60 YIKGEGTQK----HIGKILEFF--KTTDGEE-----YFRVQWFYRAEDTVMKEAADFHDR 108
YIKG IG+I E F K ++G RV FYR E+T A +H
Sbjct: 381 YIKGSNLDAPEPYRIGRIKEIFCPKKSNGRPNETDIKIRVNKFYRPENTHKSTPASYHAD 440
Query: 109 KRLFY----STVMNDNPVDCIISKVIVAQIPPKIGLKSNSIPSSDFYFDMEYCVEYSTFR 164
L Y V++ V + +P + + S P+ FYF Y + +F
Sbjct: 441 INLLYWSDEEAVVDFKAVQGRCTVEYGEDLPECVQVYSMGGPNR-FYFLEAYNAKSKSFE 499
Query: 165 TLLTGKIHDLSLPSCTETVPTTATSTFFE-NMPNHGPHKAELALLDLYSGCGGMSTGLCL 223
+ S E + P +L LD++SGCGG+S G
Sbjct: 500 DPPNHARSPGNKGKGKGKGKGKPKSQACEPSEPEIEIKLPKLRTLDVFSGCGGLSEGF-H 558
Query: 224 GAKLSCTNLVTRWALDSDKSACESLKLNHPEAQVRNEAAEDFLELV 269
A +S T WA++ A ++ +LN+P + V E L+LV
Sbjct: 559 QAGIS----DTLWAIEMWDPAAQAFRLNNPGSTVFTEDCNILLKLV 600
Score = 32.7 bits (73), Expect = 0.48, Method: Compositional matrix adjust.
Identities = 28/136 (20%), Positives = 57/136 (41%), Gaps = 15/136 (11%)
Query: 42 HYAQARIGECIFDLGDCAYIKGEGTQK--HIGKILEFFKTTDGEEYFRVQWFYRAEDTVM 99
+Y + I ++GDC + + + K ++ ++ ++ + + F WF DTV+
Sbjct: 148 YYKKVCIDAETLEVGDCVSVIPDDSSKPLYLARVTALWEDSSNGQMFHAHWFCAGTDTVL 207
Query: 100 KEAADFHDRKRLFYSTVMNDNPVDCIISKVIVAQIPP------KIGLKSNSIPSSD---- 149
+D + LF D + I SKV V P + G+ S+ D
Sbjct: 208 GATSDPLE---LFLVDECEDMQLSYIHSKVKVIYKAPSENWAMEGGMDPESLLEGDDGKT 264
Query: 150 FYFDMEYCVEYSTFRT 165
+++ + Y +Y+ F +
Sbjct: 265 YFYQLWYDQDYARFES 280
>pdb|3PTA|A Chain A, Crystal Structure Of Human Dnmt1(646-1600) In Complex With
Dna
Length = 956
Score = 90.9 bits (224), Expect = 2e-18, Method: Compositional matrix adjust.
Identities = 42/108 (38%), Positives = 66/108 (61%), Gaps = 2/108 (1%)
Query: 414 KSKILPLPGDVDVICGGPPCQGISGYNRFRNVDSPLDDERNRQIVIFMDIVEFLKPKYVL 473
+ + LP GDV+++CGGPPCQG SG NRF + +N +V F+ ++ +P++ L
Sbjct: 563 RGQRLPQKGDVEMLCGGPPCQGFSGMNRFNS--RTYSKFKNSLVVSFLSYCDYYRPRFFL 620
Query: 474 MENVVDILKFDKASLGRYALSRLVHMKYQARFGIIAAGCYGLPQFRLR 521
+ENV + + F ++ + + L LV M YQ FG++ AG YG+ Q R R
Sbjct: 621 LENVRNFVSFKRSMVLKLTLRCLVRMGYQCTFGVLQAGQYGVAQTRRR 668
Score = 43.9 bits (102), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 59/226 (26%), Positives = 88/226 (38%), Gaps = 22/226 (9%)
Query: 60 YIKGEGTQK----HIGKILEFF--KTTDGEE-----YFRVQWFYRAEDTVMKEAADFHDR 108
YIKG IG+I E F K ++G RV FYR E+T A +H
Sbjct: 335 YIKGSNLDAPEPYRIGRIKEIFCPKKSNGRPNETDIKIRVNKFYRPENTHKSTPASYHAD 394
Query: 109 KRLFY----STVMNDNPVDCIISKVIVAQIPPKIGLKSNSIPSSDFYFDMEYCVEYSTFR 164
L Y V++ V + +P + + S P+ FYF Y + +F
Sbjct: 395 INLLYWSDEEAVVDFKAVQGRCTVEYGEDLPECVQVYSMGGPNR-FYFLEAYNAKSKSFE 453
Query: 165 TLLTGKIHDLSLPSCTETVPTTATSTFFE-NMPNHGPHKAELALLDLYSGCGGMSTGLCL 223
+ S E + P +L LD++SGCGG+S G
Sbjct: 454 DPPNHARSPGNKGKGKGKGKGKPKSQACEPSEPEIEIKLPKLRTLDVFSGCGGLSEGF-H 512
Query: 224 GAKLSCTNLVTRWALDSDKSACESLKLNHPEAQVRNEAAEDFLELV 269
A +S T WA++ A ++ +LN+P + V E L+LV
Sbjct: 513 QAGIS----DTLWAIEMWDPAAQAFRLNNPGSTVFTEDCNILLKLV 554
Score = 33.1 bits (74), Expect = 0.40, Method: Compositional matrix adjust.
Identities = 28/136 (20%), Positives = 57/136 (41%), Gaps = 15/136 (11%)
Query: 42 HYAQARIGECIFDLGDCAYIKGEGTQK--HIGKILEFFKTTDGEEYFRVQWFYRAEDTVM 99
+Y + I ++GDC + + + K ++ ++ ++ + + F WF DTV+
Sbjct: 102 YYKKVCIDAETLEVGDCVSVIPDDSSKPLYLARVTALWEDSSNGQMFHAHWFCAGTDTVL 161
Query: 100 KEAADFHDRKRLFYSTVMNDNPVDCIISKVIVAQIPP------KIGLKSNSIPSSD---- 149
+D + LF D + I SKV V P + G+ S+ D
Sbjct: 162 GATSDPLE---LFLVDECEDMQLSYIHSKVKVIYKAPSENWAMEGGMDPESLLEGDDGKT 218
Query: 150 FYFDMEYCVEYSTFRT 165
+++ + Y +Y+ F +
Sbjct: 219 YFYQLWYDQDYARFES 234
>pdb|3AV4|A Chain A, Crystal Structure Of Mouse Dna Methyltransferase 1
pdb|3AV5|A Chain A, Crystal Structure Of Mouse Dna Methyltransferase 1 With
Adohcy
pdb|3AV6|A Chain A, Crystal Structure Of Mouse Dna Methyltransferase 1 With
Adomet
Length = 1330
Score = 89.4 bits (220), Expect = 4e-18, Method: Compositional matrix adjust.
Identities = 41/104 (39%), Positives = 64/104 (61%), Gaps = 2/104 (1%)
Query: 418 LPLPGDVDVICGGPPCQGISGYNRFRNVDSPLDDERNRQIVIFMDIVEFLKPKYVLMENV 477
LP GDV+++CGGPPCQG SG NRF + +N +V F+ ++ +P++ L+ENV
Sbjct: 924 LPQKGDVEMLCGGPPCQGFSGMNRFNS--RTYSKFKNSLVVSFLSYCDYYRPRFFLLENV 981
Query: 478 VDILKFDKASLGRYALSRLVHMKYQARFGIIAAGCYGLPQFRLR 521
+ + + ++ + + L LV M YQ FG++ AG YG+ Q R R
Sbjct: 982 RNFVSYRRSMVLKLTLRCLVRMGYQCTFGVLQAGQYGVAQTRRR 1025
Score = 38.9 bits (89), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 24/66 (36%), Positives = 36/66 (54%), Gaps = 5/66 (7%)
Query: 204 ELALLDLYSGCGGMSTGLCLGAKLSCTNLVTRWALDSDKSACESLKLNHPEAQVRNEAAE 263
+L LD++SGCGG+S G A +S T WA++ A ++ +LN+P V E
Sbjct: 851 KLRTLDVFSGCGGLSEGF-HQAGIS----ETLWAIEMWDPAAQAFRLNNPGTTVFTEDCN 905
Query: 264 DFLELV 269
L+LV
Sbjct: 906 VLLKLV 911
Score = 38.1 bits (87), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 29/137 (21%), Positives = 59/137 (43%), Gaps = 16/137 (11%)
Query: 42 HYAQARIGECIFDLGDCAYIKGEGTQK--HIGKILEFFKTTDGEEYFRVQWFYRAEDTVM 99
+Y + I E + ++GDC + + + K ++ ++ ++ +G+ F WF DTV+
Sbjct: 459 YYQKVSIDEEMLEVGDCVSVIPDDSSKPLYLARVTALWEDKNGQMMFHAHWFCAGTDTVL 518
Query: 100 KEAADFHDRKRLFYSTVMNDNPVDCIISKVIVAQIPPKIGLK-------SNSIPSSD--- 149
+D + LF + + I SKV V P ++P ++
Sbjct: 519 GATSDPLE---LFLVGECENMQLSYIHSKVKVIYKAPSENWAMEGGTDPETTLPGAEDGK 575
Query: 150 -FYFDMEYCVEYSTFRT 165
++F + Y EY+ F +
Sbjct: 576 TYFFQLWYNQEYARFES 592
>pdb|3PT6|A Chain A, Crystal Structure Of Mouse Dnmt1(650-1602) In Complex With
Dna
pdb|3PT6|B Chain B, Crystal Structure Of Mouse Dnmt1(650-1602) In Complex With
Dna
Length = 954
Score = 89.0 bits (219), Expect = 5e-18, Method: Compositional matrix adjust.
Identities = 41/104 (39%), Positives = 64/104 (61%), Gaps = 2/104 (1%)
Query: 418 LPLPGDVDVICGGPPCQGISGYNRFRNVDSPLDDERNRQIVIFMDIVEFLKPKYVLMENV 477
LP GDV+++CGGPPCQG SG NRF + +N +V F+ ++ +P++ L+ENV
Sbjct: 566 LPQKGDVEMLCGGPPCQGFSGMNRFNS--RTYSKFKNSLVVSFLSYCDYYRPRFFLLENV 623
Query: 478 VDILKFDKASLGRYALSRLVHMKYQARFGIIAAGCYGLPQFRLR 521
+ + + ++ + + L LV M YQ FG++ AG YG+ Q R R
Sbjct: 624 RNFVSYRRSMVLKLTLRCLVRMGYQCTFGVLQAGQYGVAQTRRR 667
Score = 38.9 bits (89), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 24/66 (36%), Positives = 36/66 (54%), Gaps = 5/66 (7%)
Query: 204 ELALLDLYSGCGGMSTGLCLGAKLSCTNLVTRWALDSDKSACESLKLNHPEAQVRNEAAE 263
+L LD++SGCGG+S G A +S T WA++ A ++ +LN+P V E
Sbjct: 493 KLRTLDVFSGCGGLSEGF-HQAGIS----ETLWAIEMWDPAAQAFRLNNPGTTVFTEDCN 547
Query: 264 DFLELV 269
L+LV
Sbjct: 548 VLLKLV 553
Score = 38.5 bits (88), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 29/137 (21%), Positives = 59/137 (43%), Gaps = 16/137 (11%)
Query: 42 HYAQARIGECIFDLGDCAYIKGEGTQK--HIGKILEFFKTTDGEEYFRVQWFYRAEDTVM 99
+Y + I E + ++GDC + + + K ++ ++ ++ +G+ F WF DTV+
Sbjct: 101 YYQKVSIDEEMLEVGDCVSVIPDDSSKPLYLARVTALWEDKNGQMMFHAHWFCAGTDTVL 160
Query: 100 KEAADFHDRKRLFYSTVMNDNPVDCIISKVIVAQIPPKIGLK-------SNSIPSSD--- 149
+D + LF + + I SKV V P ++P ++
Sbjct: 161 GATSDPLE---LFLVGECENMQLSYIHSKVKVIYKAPSENWAMEGGTDPETTLPGAEDGK 217
Query: 150 -FYFDMEYCVEYSTFRT 165
++F + Y EY+ F +
Sbjct: 218 TYFFQLWYNQEYARFES 234
>pdb|3PT9|A Chain A, Crystal Structure Of Mouse Dnmt1(731-1602) In The Free
State
pdb|4DA4|A Chain A, Structure Of Mouse Dnmt1 (731-1602) Bound To
Hemimethylated Cpg Dna
pdb|4DA4|B Chain B, Structure Of Mouse Dnmt1 (731-1602) Bound To
Hemimethylated Cpg Dna
Length = 873
Score = 89.0 bits (219), Expect = 6e-18, Method: Compositional matrix adjust.
Identities = 41/104 (39%), Positives = 64/104 (61%), Gaps = 2/104 (1%)
Query: 418 LPLPGDVDVICGGPPCQGISGYNRFRNVDSPLDDERNRQIVIFMDIVEFLKPKYVLMENV 477
LP GDV+++CGGPPCQG SG NRF + +N +V F+ ++ +P++ L+ENV
Sbjct: 485 LPQKGDVEMLCGGPPCQGFSGMNRFNS--RTYSKFKNSLVVSFLSYCDYYRPRFFLLENV 542
Query: 478 VDILKFDKASLGRYALSRLVHMKYQARFGIIAAGCYGLPQFRLR 521
+ + + ++ + + L LV M YQ FG++ AG YG+ Q R R
Sbjct: 543 RNFVSYRRSMVLKLTLRCLVRMGYQCTFGVLQAGQYGVAQTRRR 586
Score = 38.9 bits (89), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 24/66 (36%), Positives = 36/66 (54%), Gaps = 5/66 (7%)
Query: 204 ELALLDLYSGCGGMSTGLCLGAKLSCTNLVTRWALDSDKSACESLKLNHPEAQVRNEAAE 263
+L LD++SGCGG+S G A +S T WA++ A ++ +LN+P V E
Sbjct: 412 KLRTLDVFSGCGGLSEGF-HQAGIS----ETLWAIEMWDPAAQAFRLNNPGTTVFTEDCN 466
Query: 264 DFLELV 269
L+LV
Sbjct: 467 VLLKLV 472
Score = 38.5 bits (88), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 29/137 (21%), Positives = 59/137 (43%), Gaps = 16/137 (11%)
Query: 42 HYAQARIGECIFDLGDCAYIKGEGTQK--HIGKILEFFKTTDGEEYFRVQWFYRAEDTVM 99
+Y + I E + ++GDC + + + K ++ ++ ++ +G+ F WF DTV+
Sbjct: 20 YYQKVSIDEEMLEVGDCVSVIPDDSSKPLYLARVTALWEDKNGQMMFHAHWFCAGTDTVL 79
Query: 100 KEAADFHDRKRLFYSTVMNDNPVDCIISKVIVAQIPPKIGLK-------SNSIPSSD--- 149
+D + LF + + I SKV V P ++P ++
Sbjct: 80 GATSDPLE---LFLVGECENMQLSYIHSKVKVIYKAPSENWAMEGGTDPETTLPGAEDGK 136
Query: 150 -FYFDMEYCVEYSTFRT 165
++F + Y EY+ F +
Sbjct: 137 TYFFQLWYNQEYARFES 153
>pdb|3G7U|A Chain A, Crystal Structure Of Putative Dna Modification
Methyltransferase Encoded Within Prophage Cp-933r
(E.Coli)
Length = 376
Score = 48.1 bits (113), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 40/116 (34%), Positives = 56/116 (48%), Gaps = 12/116 (10%)
Query: 407 EFVRNGFKSKILPLPGDVDVICGGPPCQGISGYNRFRNVDSPLDDERNRQIVIFMDIVEF 466
E ++ FK+ + +D I GGPPCQG S + +P DD RN+ + F +V
Sbjct: 60 EIIKGFFKNDM-----PIDGIIGGPPCQGFSSIGK----GNP-DDSRNQLYMHFYRLVSE 109
Query: 467 LKPKYVLMENVVDILKFDKASLGRYALSRLVHMKYQARFGI-IAAGCYGLPQFRLR 521
L+P + L ENV I++ +K S R LV Y I + A YG P R R
Sbjct: 110 LQPLFFLAENVPGIMQ-EKYSGIRNKAFNLVSGDYDILDPIKVKASDYGAPTIRTR 164
>pdb|4HAE|A Chain A, Crystal Structure Of The Cdyl2-Chromodomain
Length = 81
Score = 48.1 bits (113), Expect = 1e-05, Method: Composition-based stats.
Identities = 25/54 (46%), Positives = 32/54 (59%), Gaps = 5/54 (9%)
Query: 355 YEVARIVDICYGDPNESGKRGLNFKVHWKGYSTSEDSWEPIEGLRNCPERIKEF 408
YEV RIVD N+ GK + + WKGY ++ED+WEP L +C E I EF
Sbjct: 24 YEVERIVD---KRKNKKGK--WEYLIRWKGYGSTEDTWEPEHHLLHCEEFIDEF 72
>pdb|2DNT|A Chain A, Solution Structure Of Rsgi Ruh-064, A Chromo Domain From
Human Cdna
Length = 78
Score = 47.0 bits (110), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 26/56 (46%), Positives = 33/56 (58%), Gaps = 5/56 (8%)
Query: 355 YEVARIVDICYGDPNESGKRGLNFKVHWKGYSTSEDSWEPIEGLRNCPERIKEFVR 410
YEV RIVD N+ GK + V WKGY + +D+WEP + L NC E I +F R
Sbjct: 14 YEVERIVD---KRKNKKGK--TEYLVRWKGYDSEDDTWEPEQHLVNCEEYIHDFNR 64
>pdb|2UYH|A Chain A, Hhai Dna Methyltransferase S87q-Q237s Mutant Complex With
13mer Gcgc-Gmgc Oligonucleotide And Sah
Length = 327
Score = 45.1 bits (105), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 29/99 (29%), Positives = 41/99 (41%), Gaps = 4/99 (4%)
Query: 423 DVDVICGGPPCQGISGYNRFRNVDSPLDDERNRQIVIFMDIVEFLKPKYVLMENVVDILK 482
D D++C G PCQ S + +D R IV KPK V MENV +
Sbjct: 71 DHDILCAGFPCQAFS----IQGKQKGFEDSRGTLFFDIARIVREKKPKVVFMENVKNFAS 126
Query: 483 FDKASLGRYALSRLVHMKYQARFGIIAAGCYGLPQFRLR 521
D + + + + Y ++ A YG+PQ R R
Sbjct: 127 HDNGNTLEVVKNTMNELDYSFHAKVLNALDYGIPQKRER 165
>pdb|3QO2|A Chain A, Structural Insights For Mpp8 Chromodomain Interaction With
Histone H3 Lysine 9
pdb|3QO2|B Chain B, Structural Insights For Mpp8 Chromodomain Interaction With
Histone H3 Lysine 9
pdb|3QO2|C Chain C, Structural Insights For Mpp8 Chromodomain Interaction With
Histone H3 Lysine 9
pdb|3QO2|D Chain D, Structural Insights For Mpp8 Chromodomain Interaction With
Histone H3 Lysine 9
Length = 64
Score = 44.7 bits (104), Expect = 1e-04, Method: Composition-based stats.
Identities = 22/54 (40%), Positives = 34/54 (62%), Gaps = 6/54 (11%)
Query: 355 YEVARIVDICYGDPNESGKRGLNFKVHWKGYSTSEDSWEPIEGLRNCPERIKEF 408
+EV +I+D+ E GK + +KV WKGY++ +D+WEP L +C E + EF
Sbjct: 7 FEVEKILDM----KTEGGK--VLYKVRWKGYTSDDDTWEPEIHLEDCKEVLLEF 54
>pdb|1SVU|A Chain A, Structure Of The Q237w Mutant Of Hhai Dna
Methyltransferase: An Insight Into Protein-Protein
Interactions
pdb|1SVU|B Chain B, Structure Of The Q237w Mutant Of Hhai Dna
Methyltransferase: An Insight Into Protein-Protein
Interactions
Length = 327
Score = 44.3 bits (103), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 29/99 (29%), Positives = 40/99 (40%), Gaps = 4/99 (4%)
Query: 423 DVDVICGGPPCQGISGYNRFRNVDSPLDDERNRQIVIFMDIVEFLKPKYVLMENVVDILK 482
D D++C G PCQ S +D R IV KPK V MENV +
Sbjct: 71 DHDILCAGFPCQAFS----ISGKQKGFEDSRGTLFFDIARIVREKKPKVVFMENVKNFAS 126
Query: 483 FDKASLGRYALSRLVHMKYQARFGIIAAGCYGLPQFRLR 521
D + + + + Y ++ A YG+PQ R R
Sbjct: 127 HDNGNTLEVVKNTMNELDYSFHAKVLNALDYGIPQKRER 165
>pdb|3LWE|A Chain A, The Crystal Structure Of Mpp8
pdb|3LWE|B Chain B, The Crystal Structure Of Mpp8
pdb|3R93|A Chain A, Crystal Structure Of The Chromo Domain Of M-Phase
Phosphoprotein 8 Bound To H3k9me3 Peptide
pdb|3R93|B Chain B, Crystal Structure Of The Chromo Domain Of M-Phase
Phosphoprotein 8 Bound To H3k9me3 Peptide
pdb|3R93|C Chain C, Crystal Structure Of The Chromo Domain Of M-Phase
Phosphoprotein 8 Bound To H3k9me3 Peptide
pdb|3R93|D Chain D, Crystal Structure Of The Chromo Domain Of M-Phase
Phosphoprotein 8 Bound To H3k9me3 Peptide
pdb|3SVM|A Chain A, Human Mpp8 - Human Dnmt3ak47me2 Peptide
Length = 62
Score = 44.3 bits (103), Expect = 2e-04, Method: Composition-based stats.
Identities = 22/54 (40%), Positives = 34/54 (62%), Gaps = 6/54 (11%)
Query: 355 YEVARIVDICYGDPNESGKRGLNFKVHWKGYSTSEDSWEPIEGLRNCPERIKEF 408
+EV +I+D+ E GK + +KV WKGY++ +D+WEP L +C E + EF
Sbjct: 5 FEVEKILDM----KTEGGK--VLYKVRWKGYTSDDDTWEPEIHLEDCKEVLLEF 52
>pdb|1MHT|A Chain A, Covalent Ternary Structure Of Hhai Methyltransferase, Dna
And S-Adenosyl-L-Homocysteine
pdb|3MHT|A Chain A, Ternary Structure Of Hhai Methyltransferase With
Unmodified Dna And Adohcy
pdb|4MHT|A Chain A, Ternary Structure Of Hhai Methyltransferase With Native
Dna And Adohcy
pdb|5MHT|A Chain A, Ternary Structure Of Hhai Methyltransferase With
Hemimethylated Dna And Adohcy
pdb|6MHT|A Chain A, Ternary Structure Of Hhai Methyltransferase With Adohcy
And Dna Containing 4'-Thio-2'deoxycytidine At The Target
pdb|7MHT|A Chain A, Cytosine-Specific Methyltransferase HhaiDNA COMPLEX
pdb|8MHT|A Chain A, Cytosine-Specific Methyltransferase HhaiDNA COMPLEX
pdb|9MHT|A Chain A, Cytosine-specific Methyltransferase Hhai/dna Complex
pdb|10MH|A Chain A, Ternary Structure Of Hhai Methyltransferase With Adohcy
And Hemimethylated Dna Containing
5,6-Dihydro-5-Azacytosine At The Target
pdb|2HMY|B Chain B, Binary Complex Of Hhai Methyltransferase With Adomet
Formed In The Presence Of A Short Nonpsecific Dna
Oligonucleotide
pdb|1M0E|A Chain A, Zebularine: A Novel Dna Methylation Inhibitor That Forms A
Covalent Complex With Dna Methyltransferase
pdb|1SKM|A Chain A, Hhai Methyltransferase In Complex With Dna Containing An
Abasic South Carbocyclic Sugar At Its Target Site
pdb|2C7O|A Chain A, Hhai Dna Methyltransferase Complex With 13mer
Oligonucleotide Containing 2-Aminopurine Adjacent To The
Target Base (Pcgc:gmgc) And Sah
pdb|2C7P|A Chain A, Hhai Dna Methyltransferase Complex With Oligonucleotide
Containing 2-Aminopurine Opposite To The Target Base (
Gcgc:gmpc) And Sah
pdb|2C7Q|A Chain A, Hhai Dna Methyltransferase Complex With Oligonucleotide
Containing 2-Aminopurine Outside The Recognition
Sequence (Paired With G) And Sah
pdb|2HR1|A Chain A, Ternary Structure Of Wt M.hhai C5-cytosine Dna
Methyltransferase With Unmodified Dna And Adohcy
pdb|1HMY|A Chain A, Crystal Structure Of The Hhai Dna Methyltransferase
Complexed With S- Adenosyl-L-Methionine
pdb|3EEO|A Chain A, M. Hhai Co-Crystallized With Synthetic Dsdna Containing A
Propane Diol In Place Of The Deoxycytidine Residue
Targeted For Methylation
Length = 327
Score = 44.3 bits (103), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 29/99 (29%), Positives = 40/99 (40%), Gaps = 4/99 (4%)
Query: 423 DVDVICGGPPCQGISGYNRFRNVDSPLDDERNRQIVIFMDIVEFLKPKYVLMENVVDILK 482
D D++C G PCQ S +D R IV KPK V MENV +
Sbjct: 71 DHDILCAGFPCQAFS----ISGKQKGFEDSRGTLFFDIARIVREKKPKVVFMENVKNFAS 126
Query: 483 FDKASLGRYALSRLVHMKYQARFGIIAAGCYGLPQFRLR 521
D + + + + Y ++ A YG+PQ R R
Sbjct: 127 HDNGNTLEVVKNTMNELDYSFHAKVLNALDYGIPQKRER 165
>pdb|1FJX|A Chain A, Structure Of Ternary Complex Of Hhai Methyltransferase
Mutant (T250g) In Complex With Dna And Adohcy
pdb|2C7R|A Chain A, Hhai Dna Methyltransferase (T250g Mutant) Complex With
Oligonucleotide Containing 2-Aminopurine As A Target
Base (Gpgc:gmgc) And Sah
Length = 327
Score = 43.9 bits (102), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 29/99 (29%), Positives = 40/99 (40%), Gaps = 4/99 (4%)
Query: 423 DVDVICGGPPCQGISGYNRFRNVDSPLDDERNRQIVIFMDIVEFLKPKYVLMENVVDILK 482
D D++C G PCQ S +D R IV KPK V MENV +
Sbjct: 71 DHDILCAGFPCQAFS----ISGKQKGFEDSRGTLFFDIARIVREKKPKVVFMENVKNFAS 126
Query: 483 FDKASLGRYALSRLVHMKYQARFGIIAAGCYGLPQFRLR 521
D + + + + Y ++ A YG+PQ R R
Sbjct: 127 HDNGNTLEVVKNTMNELDYSFHAKVLNALDYGIPQKRER 165
>pdb|2I9K|A Chain A, Engineered Extrahelical Base Destabilization Enhances
Sequence Discrimination Of Dna Methyltransferase M.Hhai
Length = 327
Score = 43.5 bits (101), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 29/99 (29%), Positives = 40/99 (40%), Gaps = 4/99 (4%)
Query: 423 DVDVICGGPPCQGISGYNRFRNVDSPLDDERNRQIVIFMDIVEFLKPKYVLMENVVDILK 482
D D++C G PCQ S +D R IV KPK V MENV +
Sbjct: 71 DHDILCAGFPCQAFS----ISGKQKGFEDSRGTLFFDIARIVREKKPKVVFMENVKNAAS 126
Query: 483 FDKASLGRYALSRLVHMKYQARFGIIAAGCYGLPQFRLR 521
D + + + + Y ++ A YG+PQ R R
Sbjct: 127 HDNGNTLEVVKNTMNELDYSFHAKVLNALDYGIPQKRER 165
>pdb|2UZ4|A Chain A, Hhai Dna Methyltransferase R165n Mutant Complex With 13mer
Gcgc-Gmgc Oligonucleotide And Sah
Length = 327
Score = 43.1 bits (100), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 28/97 (28%), Positives = 39/97 (40%), Gaps = 4/97 (4%)
Query: 423 DVDVICGGPPCQGISGYNRFRNVDSPLDDERNRQIVIFMDIVEFLKPKYVLMENVVDILK 482
D D++C G PCQ S +D R IV KPK V MENV +
Sbjct: 71 DHDILCAGFPCQAFS----ISGKQKGFEDSRGTLFFDIARIVREKKPKVVFMENVKNFAS 126
Query: 483 FDKASLGRYALSRLVHMKYQARFGIIAAGCYGLPQFR 519
D + + + + Y ++ A YG+PQ R
Sbjct: 127 HDNGNTLEVVKNTMNELDYSFHAKVLNALDYGIPQKR 163
>pdb|2Z6Q|A Chain A, Ternary Structure Of Arg165ala M.Hhai C5-Cytosine Dna
Methyltransferase With Unmodified Dna And Adohcy
Length = 327
Score = 43.1 bits (100), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 28/97 (28%), Positives = 39/97 (40%), Gaps = 4/97 (4%)
Query: 423 DVDVICGGPPCQGISGYNRFRNVDSPLDDERNRQIVIFMDIVEFLKPKYVLMENVVDILK 482
D D++C G PCQ S +D R IV KPK V MENV +
Sbjct: 71 DHDILCAGFPCQAFS----ISGKQKGFEDSRGTLFFDIARIVREKKPKVVFMENVKNFAS 126
Query: 483 FDKASLGRYALSRLVHMKYQARFGIIAAGCYGLPQFR 519
D + + + + Y ++ A YG+PQ R
Sbjct: 127 HDNGNTLEVVKNTMNELDYSFHAKVLNALDYGIPQKR 163
>pdb|2ZCJ|A Chain A, Ternary Structure Of The Glu119gln M.Hhai, C5-Cytosine Dna
Methyltransferase, With Unmodified Dna And Adohcy
Length = 327
Score = 42.7 bits (99), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 28/99 (28%), Positives = 40/99 (40%), Gaps = 4/99 (4%)
Query: 423 DVDVICGGPPCQGISGYNRFRNVDSPLDDERNRQIVIFMDIVEFLKPKYVLMENVVDILK 482
D D++C G PCQ S +D R IV KPK V M+NV +
Sbjct: 71 DHDILCAGFPCQAFS----ISGKQKGFEDSRGTLFFDIARIVREKKPKVVFMQNVKNFAS 126
Query: 483 FDKASLGRYALSRLVHMKYQARFGIIAAGCYGLPQFRLR 521
D + + + + Y ++ A YG+PQ R R
Sbjct: 127 HDNGNTLEVVKNTMNELDYSFHAKVLNALDYGIPQKRER 165
>pdb|2UYC|A Chain A, Hhai Dna Methyltransferase R163n Mutant Complex With 13mer
Gcgc-Gmgc Oligonucleotide And Sah
Length = 327
Score = 42.4 bits (98), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 27/95 (28%), Positives = 38/95 (40%), Gaps = 4/95 (4%)
Query: 423 DVDVICGGPPCQGISGYNRFRNVDSPLDDERNRQIVIFMDIVEFLKPKYVLMENVVDILK 482
D D++C G PCQ S +D R IV KPK V MENV +
Sbjct: 71 DHDILCAGFPCQAFS----ISGKQKGFEDSRGTLFFDIARIVREKKPKVVFMENVKNFAS 126
Query: 483 FDKASLGRYALSRLVHMKYQARFGIIAAGCYGLPQ 517
D + + + + Y ++ A YG+PQ
Sbjct: 127 HDNGNTLEVVKNTMNELDYSFHAKVLNALDYGIPQ 161
>pdb|2Z6U|A Chain A, Ternary Structure Of The Glu119ala M.Hhai, C5-Cytosine Dna
Methyltransferase, With Unmodified Dna And Adohcy
Length = 327
Score = 42.0 bits (97), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 28/99 (28%), Positives = 39/99 (39%), Gaps = 4/99 (4%)
Query: 423 DVDVICGGPPCQGISGYNRFRNVDSPLDDERNRQIVIFMDIVEFLKPKYVLMENVVDILK 482
D D++C G PCQ S +D R IV KPK V M NV +
Sbjct: 71 DHDILCAGFPCQAFS----ISGKQKGFEDSRGTLFFDIARIVREKKPKVVFMANVKNFAS 126
Query: 483 FDKASLGRYALSRLVHMKYQARFGIIAAGCYGLPQFRLR 521
D + + + + Y ++ A YG+PQ R R
Sbjct: 127 HDNGNTLEVVKNTMNELDYSFHAKVLNALDYGIPQKRER 165
>pdb|2Z6A|A Chain A, S-Adenosyl-L-Methionine-Dependent Methyl Transfer:
Observable Precatalytic Intermediates During Dna
Cytosine Methylation
Length = 327
Score = 40.8 bits (94), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 28/99 (28%), Positives = 39/99 (39%), Gaps = 4/99 (4%)
Query: 423 DVDVICGGPPCQGISGYNRFRNVDSPLDDERNRQIVIFMDIVEFLKPKYVLMENVVDILK 482
D D++C G P Q S +D R IV KPK V MENV +
Sbjct: 71 DHDILCAGFPAQAFS----ISGKQKGFEDSRGTLFFDIARIVREKKPKVVFMENVKNFAS 126
Query: 483 FDKASLGRYALSRLVHMKYQARFGIIAAGCYGLPQFRLR 521
D + + + + Y ++ A YG+PQ R R
Sbjct: 127 HDNGNTLEVVKNTMNELDYSFHAKVLNALDYGIPQKRER 165
>pdb|1DCT|A Chain A, Dna (Cytosine-5) Methylase From Haeiii Covalently Bound To
Dna
pdb|1DCT|B Chain B, Dna (Cytosine-5) Methylase From Haeiii Covalently Bound To
Dna
Length = 324
Score = 40.0 bits (92), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 27/97 (27%), Positives = 42/97 (43%), Gaps = 4/97 (4%)
Query: 425 DVICGGPPCQGISGYNRFRNVDSPLDDERNRQIVIFMDIVEFLKPKYVLMENVVDILKFD 484
D I GGPPCQ S R +D P R + ++ I++ KP + L ENV ++
Sbjct: 63 DGIIGGPPCQSWSEGGSLRGIDDP----RGKLFYEYIRILKQKKPIFFLAENVKGMMAQR 118
Query: 485 KASLGRYALSRLVHMKYQARFGIIAAGCYGLPQFRLR 521
+ + + Y ++ A YG+ Q R R
Sbjct: 119 HNKAVQEFIQEFDNAGYDVHIILLNANDYGVAQDRKR 155
>pdb|3F2U|A Chain A, Crystal Structure Of Human Chromobox Homolog 1 (Cbx1)
Length = 55
Score = 39.3 bits (90), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 20/59 (33%), Positives = 35/59 (59%), Gaps = 7/59 (11%)
Query: 353 GEYEVARIVDICYGDPNESGKRGLNFKVHWKGYSTSEDSWEPIEGLRNCPERIKEFVRN 411
GEY V +++D K + + + WKG+S +++WEP E L +CP+ I EF+++
Sbjct: 1 GEYVVEKVLD------RRVVKGKVEYLLKWKGFSDEDNTWEPEENL-DCPDLIAEFLQS 52
>pdb|1G55|A Chain A, Structure Of Human Dnmt2, An Enigmatic Dna
Methyltransferase Homologue
Length = 343
Score = 38.9 bits (89), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 27/99 (27%), Positives = 47/99 (47%), Gaps = 9/99 (9%)
Query: 425 DVICGGPPCQGISGYNRFRNVDSPLDDERNRQIVIFMDIVEFLK--PKYVLMENVVDILK 482
D+I PPCQ + R + D R + +DI+ L+ PKY+L+ENV
Sbjct: 70 DMILMSPPCQPFTRIGR----QGDMTDSRTNSFLHILDILPRLQKLPKYILLENVKG--- 122
Query: 483 FDKASLGRYALSRLVHMKYQARFGIIAAGCYGLPQFRLR 521
F+ +S + + + +Q + +++ G+P RLR
Sbjct: 123 FEVSSTRDLLIQTIENXGFQYQEFLLSPTSLGIPNSRLR 161
Score = 34.7 bits (78), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 21/59 (35%), Positives = 28/59 (47%), Gaps = 4/59 (6%)
Query: 205 LALLDLYSGCGGMSTGLCLGAKLSCTNLVTRWALDSDKSACESLKLNHPEAQVRNEAAE 263
L +L+LYSG GGM L + SC A+D + A E K N P Q+ + E
Sbjct: 3 LRVLELYSGVGGMHHAL----RESCIPAQVVAAIDVNTVANEVYKYNFPHTQLLAKTIE 57
>pdb|3TZD|A Chain A, Crystal Structure Of The Complex Of Human Chromobox
Homolog 3 (cbx3)
Length = 58
Score = 38.9 bits (89), Expect = 0.008, Method: Composition-based stats.
Identities = 21/63 (33%), Positives = 37/63 (58%), Gaps = 15/63 (23%)
Query: 353 GEYEVARIVDICYGDPNESGKRGLNFKVH----WKGYSTSEDSWEPIEGLRNCPERIKEF 408
GE+ V +++D +R +N KV WKG++ ++++WEP E L +CPE I+ F
Sbjct: 5 GEFVVEKVLD----------RRVVNGKVEYFLKWKGFTDADNTWEPEENL-DCPELIEAF 53
Query: 409 VRN 411
+ +
Sbjct: 54 LNS 56
>pdb|1W4S|A Chain A, Crystal Structure Of The Proximal Bah Domain Of Polybromo
Length = 174
Score = 38.1 bits (87), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 27/102 (26%), Positives = 44/102 (43%), Gaps = 3/102 (2%)
Query: 52 IFDLGDCAYIK--GEGTQKHIGKILEFFKTTDGEEYFRVQWFYRAEDTVMKEAADFHDRK 109
++ +GD Y++ Q HI I ++ + GE++ WFYR +T F + K
Sbjct: 26 MYHVGDYVYVEPAEANLQPHIVCIERLWEDSAGEKWLYGCWFYRPNETFHLATRKFLE-K 84
Query: 110 RLFYSTVMNDNPVDCIISKVIVAQIPPKIGLKSNSIPSSDFY 151
+F S N PV I+ K +V + L + D Y
Sbjct: 85 EVFKSDYYNKVPVSKILGKCVVMFVKEYFKLCPENFRDEDVY 126
>pdb|1G6Z|A Chain A, Solution Structure Of The Clr4 Chromo Domain
Length = 70
Score = 37.7 bits (86), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 22/57 (38%), Positives = 31/57 (54%), Gaps = 4/57 (7%)
Query: 354 EYEVARIVDICYGDPNESGKRGLNFKVHWKGYSTSEDSWEPIEGLRNCPERIKEFVR 410
EYEV RIVD + +G L +++ W YS+ D+WEP E L C + E+ R
Sbjct: 8 EYEVERIVD---EKLDRNGAVKL-YRIRWLNYSSRSDTWEPPENLSGCSAVLAEWKR 60
>pdb|1AP0|A Chain A, Structure Of The Chromatin Binding (Chromo) Domain From
Mouse Modifier Protein 1, Nmr, 26 Structures
pdb|1GUW|A Chain A, Structure Of The Chromodomain From Mouse Hp1beta In
Complex With The Lysine 9-Methyl Histone H3 N-Terminal
Peptide, Nmr, 25 Structures
Length = 73
Score = 37.7 bits (86), Expect = 0.018, Method: Composition-based stats.
Identities = 15/39 (38%), Positives = 27/39 (69%), Gaps = 1/39 (2%)
Query: 373 KRGLNFKVHWKGYSTSEDSWEPIEGLRNCPERIKEFVRN 411
K + + + WKG+S +++WEP E L +CP+ I EF+++
Sbjct: 26 KGKVEYLLKWKGFSDEDNTWEPEENL-DCPDLIAEFLQS 63
>pdb|2L11|A Chain A, Solution Nmr Structure Of The Cbx3 In Complex With H3k9me3
Peptide
Length = 54
Score = 36.6 bits (83), Expect = 0.035, Method: Compositional matrix adjust.
Identities = 21/61 (34%), Positives = 36/61 (59%), Gaps = 15/61 (24%)
Query: 353 GEYEVARIVDICYGDPNESGKRGLNFKVH----WKGYSTSEDSWEPIEGLRNCPERIKEF 408
GE+ V +++D +R +N KV WKG++ ++++WEP E L +CPE I+ F
Sbjct: 1 GEFVVEKVLD----------RRVVNGKVEYFLKWKGFTDADNTWEPEENL-DCPELIEAF 49
Query: 409 V 409
+
Sbjct: 50 L 50
>pdb|3UBT|Y Chain Y, Crystal Structure Of C71s Mutant Of Dna Cytosine-5
Methyltransferase M.Haeiii Bound To Dna
pdb|3UBT|A Chain A, Crystal Structure Of C71s Mutant Of Dna Cytosine-5
Methyltransferase M.Haeiii Bound To Dna
pdb|3UBT|B Chain B, Crystal Structure Of C71s Mutant Of Dna Cytosine-5
Methyltransferase M.Haeiii Bound To Dna
Length = 331
Score = 36.6 bits (83), Expect = 0.036, Method: Compositional matrix adjust.
Identities = 26/97 (26%), Positives = 41/97 (42%), Gaps = 4/97 (4%)
Query: 425 DVICGGPPCQGISGYNRFRNVDSPLDDERNRQIVIFMDIVEFLKPKYVLMENVVDILKFD 484
D I GGPP Q S R +D P R + ++ I++ KP + L ENV ++
Sbjct: 63 DGIIGGPPSQSWSEGGSLRGIDDP----RGKLFYEYIRILKQKKPIFFLAENVKGMMAQR 118
Query: 485 KASLGRYALSRLVHMKYQARFGIIAAGCYGLPQFRLR 521
+ + + Y ++ A YG+ Q R R
Sbjct: 119 HNKAVQEFIQEFDNAGYDVHIILLNANDYGVAQDRKR 155
>pdb|3DM1|A Chain A, Crystal Structure Of The Complex Of Human Chromobox
Homolog 3 (cbx3) With Peptide
pdb|3DM1|C Chain C, Crystal Structure Of The Complex Of Human Chromobox
Homolog 3 (cbx3) With Peptide
pdb|3DM1|E Chain E, Crystal Structure Of The Complex Of Human Chromobox
Homolog 3 (cbx3) With Peptide
pdb|3DM1|G Chain G, Crystal Structure Of The Complex Of Human Chromobox
Homolog 3 (cbx3) With Peptide
Length = 58
Score = 36.2 bits (82), Expect = 0.046, Method: Composition-based stats.
Identities = 17/43 (39%), Positives = 29/43 (67%), Gaps = 5/43 (11%)
Query: 373 KRGLNFKVH----WKGYSTSEDSWEPIEGLRNCPERIKEFVRN 411
+R +N KV WKG++ ++++WEP E L +CPE I+ F+ +
Sbjct: 10 RRVVNGKVEYFLKWKGFTDADNTWEPEENL-DCPELIEAFLNS 51
>pdb|3FDT|A Chain A, Crystal Structure Of The Complex Of Human Chromobox
Homolog 5 (Cbx5) With H3k9(Me)3 Peptide
Length = 59
Score = 35.8 bits (81), Expect = 0.064, Method: Compositional matrix adjust.
Identities = 21/63 (33%), Positives = 34/63 (53%), Gaps = 7/63 (11%)
Query: 354 EYEVARIVDICYGDPNESGKRGLNFKVHWKGYSTSEDSWEPIEGLRNCPERIKEFVRNGF 413
EY V +++D K + + + WKG+S ++WEP + L +CPE I EF++
Sbjct: 3 EYVVEKVLD------RRVVKGQVEYLLKWKGFSEEHNTWEPEKNL-DCPELISEFMKKYK 55
Query: 414 KSK 416
K K
Sbjct: 56 KMK 58
>pdb|4DKJ|A Chain A, Cpg Specific Methyltransferase In Complex With Target Dna
Length = 403
Score = 33.5 bits (75), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 26/113 (23%), Positives = 48/113 (42%), Gaps = 15/113 (13%)
Query: 420 LPGDVDVICGGPPCQGISGYNRFRNVDSPLDDERNRQIVIFMDIVEFLK----------- 468
P ++D+ PCQ +S + + +D E N + + +I L+
Sbjct: 122 FPKNIDIFTYSFPCQDLS----VQGLQKGIDKELNTRSGLLWEIERILEEIKNSFSKEEM 177
Query: 469 PKYVLMENVVDILKFDKASLGRYALSRLVHMKYQARFGIIAAGCYGLPQFRLR 521
PKY+LMENV ++L L +L Y+++ ++ + + Q R R
Sbjct: 178 PKYLLMENVKNLLSHKNKKNYNTWLKQLEKFGYKSKTYLLNSKNFDNCQNRER 230
>pdb|3AMT|A Chain A, Crystal Structure Of The Tias-Trna(Ile2)-Atp Complex
Length = 440
Score = 33.5 bits (75), Expect = 0.33, Method: Compositional matrix adjust.
Identities = 23/74 (31%), Positives = 37/74 (50%), Gaps = 2/74 (2%)
Query: 449 LDDERNRQIVIFMDIVEFLKPKYVLMENVVDILKFDKA--SLGRYALSRLVHMKYQARFG 506
LDDE+ +F+D +K K + + D+L+ D+A +G+Y + L H K + G
Sbjct: 105 LDDEKTNPGAVFVDEELAVKLKPFADKAIKDVLQIDEALFVIGKYFIPHLRHKKGRGLIG 164
Query: 507 IIAAGCYGLPQFRL 520
+AA L F L
Sbjct: 165 ALAAVGAELEDFTL 178
>pdb|4H0N|A Chain A, Crystal Structure Of Spodoptera Frugiperda Dnmt2
E260a/e261a/k263a Mutant
pdb|4H0N|B Chain B, Crystal Structure Of Spodoptera Frugiperda Dnmt2
E260a/e261a/k263a Mutant
pdb|4H0N|C Chain C, Crystal Structure Of Spodoptera Frugiperda Dnmt2
E260a/e261a/k263a Mutant
pdb|4H0N|D Chain D, Crystal Structure Of Spodoptera Frugiperda Dnmt2
E260a/e261a/k263a Mutant
Length = 333
Score = 33.1 bits (74), Expect = 0.38, Method: Compositional matrix adjust.
Identities = 24/100 (24%), Positives = 46/100 (46%), Gaps = 8/100 (8%)
Query: 423 DVDVICGGPPCQGISGYNRFRNVDSPLDDERNRQIVIFMDIVEFL-KPKYVLMENVVDIL 481
+VD I PPCQ + ++ + + P R + + I++ L Y+LMENV
Sbjct: 69 NVDTILMSPPCQPFTRNGKYLDDNDP----RTNSFLYLIGILDQLDNVDYILMENVKG-- 122
Query: 482 KFDKASLGRYALSRLVHMKYQARFGIIAAGCYGLPQFRLR 521
F+ +++ + +L + + ++ G+P RLR
Sbjct: 123 -FENSTVRNLFIDKLKECNFIYQEFLLCPSTVGVPNSRLR 161
>pdb|3AMU|A Chain A, Crystal Structure Of The Tias-Trna(Ile2)-Ampcpp-Agmatine
Complex
Length = 440
Score = 32.7 bits (73), Expect = 0.54, Method: Compositional matrix adjust.
Identities = 23/74 (31%), Positives = 37/74 (50%), Gaps = 2/74 (2%)
Query: 449 LDDERNRQIVIFMDIVEFLKPKYVLMENVVDILKFDKA--SLGRYALSRLVHMKYQARFG 506
LDDE+ +F+D +K K + + D+L+ D+A +G+Y + L H K + G
Sbjct: 105 LDDEKTNPGAVFVDEELAVKLKPFADKAIKDVLQIDEALFVIGKYFIPHLRHKKGRGLIG 164
Query: 507 IIAAGCYGLPQFRL 520
+AA L F L
Sbjct: 165 ALAAVGAELEDFTL 178
>pdb|3AU7|A Chain A, Crystal Structure Of The Zrd-Deleted Mutant Of Tias In
Complex With Agmatine
Length = 402
Score = 32.3 bits (72), Expect = 0.66, Method: Compositional matrix adjust.
Identities = 23/74 (31%), Positives = 37/74 (50%), Gaps = 2/74 (2%)
Query: 449 LDDERNRQIVIFMDIVEFLKPKYVLMENVVDILKFDKA--SLGRYALSRLVHMKYQARFG 506
LDDE+ +F+D +K K + + D+L+ D+A +G+Y + L H K + G
Sbjct: 105 LDDEKTNPGAVFVDEELAVKLKPFADKAIKDVLQIDEALFVIGKYFIPHLRHKKGRGLIG 164
Query: 507 IIAAGCYGLPQFRL 520
+AA L F L
Sbjct: 165 ALAAVGAELEDFTL 178
>pdb|3EYW|A Chain A, Crystal Structure Of The C-terminal Domain Of E. Coli Kefc
In Complex With Keff
pdb|3EYW|B Chain B, Crystal Structure Of The C-terminal Domain Of E. Coli Kefc
In Complex With Keff
pdb|3L9W|A Chain A, Kefc C-Terminal Domain In Complex With Keff And Gsh
pdb|3L9W|B Chain B, Kefc C-Terminal Domain In Complex With Keff And Gsh
pdb|3L9X|A Chain A, Kefc C-Terminal Domain In Complex With Keff And Esg
pdb|3L9X|B Chain B, Kefc C-Terminal Domain In Complex With Keff And Esg
Length = 413
Score = 32.3 bits (72), Expect = 0.74, Method: Compositional matrix adjust.
Identities = 32/118 (27%), Positives = 52/118 (44%), Gaps = 22/118 (18%)
Query: 237 ALDSDKSACESLKLNHPEAQVRNEAAEDF-LELVKEWQKLCKRFAVNIVERENKQRS--- 292
AL + + A ESL L EA+ R + F +++V+E + +VE + K R+
Sbjct: 127 ALKTGRLALESLGLGPYEARERADVFRRFNIQMVEE---------MAMVENDTKARAAVY 177
Query: 293 ------MSQRVTRNSVNSPSITRNS---VDSPKVTGNSVDSPRVTRSSVNSPRVTRNS 341
+S+ +T + + I R+ + K TGN D P SS + V R S
Sbjct: 178 KRTSAMLSEIITEDREHLSLIQRHGWQGTEEGKHTGNMADEPETKPSSTSGGLVPRGS 235
>pdb|3MWY|W Chain W, Crystal Structure Of The Chromodomain-atpase Portion Of
The Yeast Chd1 Chromatin Remodeler
Length = 800
Score = 31.6 bits (70), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 18/51 (35%), Positives = 28/51 (54%), Gaps = 2/51 (3%)
Query: 370 ESGKRGLNFKVHWKGYSTSEDSWE-PIEGLRNCPERIKEFVRNGFKSKILP 419
E G L + V W+ + E +WE + ++ PE++K F +N SKILP
Sbjct: 160 EDGTSQLQYLVKWRRLNYDEATWENATDIVKLAPEQVKHF-QNRENSKILP 209
>pdb|1KNA|A Chain A, Chromo Domain Of Hp1 Complexed With Histone H3 Tail
Containing Dimethyllysine 9.
pdb|1KNE|A Chain A, Chromo Domain Of Hp1 Complexed With Histone H3 Tail
Containing Trimethyllysine 9
pdb|1Q3L|A Chain A, Chromodomain Of Hp1 Complexed With Histone H3 Tail
Containing Monomethyllysine 9
Length = 69
Score = 31.2 bits (69), Expect = 1.3, Method: Composition-based stats.
Identities = 16/54 (29%), Positives = 29/54 (53%), Gaps = 7/54 (12%)
Query: 355 YEVARIVDICYGDPNESGKRGLNFKVHWKGYSTSEDSWEPIEGLRNCPERIKEF 408
Y V +I+D K + + + WKGY +E++WEP L +C + I+++
Sbjct: 17 YAVEKIID------RRVRKGMVEYYLKWKGYPETENTWEPENNL-DCQDLIQQY 63
>pdb|3H91|A Chain A, Crystal Structure Of The Complex Of Human Chromobox
Homolog 2 (Cbx2) And H3k27 Peptide
pdb|3H91|B Chain B, Crystal Structure Of The Complex Of Human Chromobox
Homolog 2 (Cbx2) And H3k27 Peptide
Length = 54
Score = 30.8 bits (68), Expect = 2.0, Method: Composition-based stats.
Identities = 11/26 (42%), Positives = 17/26 (65%)
Query: 373 KRGLNFKVHWKGYSTSEDSWEPIEGL 398
K L + V W+G+S+ +SWEP E +
Sbjct: 16 KGKLEYLVKWRGWSSKHNSWEPEENI 41
>pdb|2D9U|A Chain A, Solution Structure Of The Chromo Domain Of Chromobox
Homolog 2 From Human
Length = 74
Score = 30.4 bits (67), Expect = 2.3, Method: Composition-based stats.
Identities = 11/26 (42%), Positives = 17/26 (65%)
Query: 373 KRGLNFKVHWKGYSTSEDSWEPIEGL 398
K L + V W+G+S+ +SWEP E +
Sbjct: 23 KGKLEYLVKWRGWSSKHNSWEPEENI 48
>pdb|2EPB|A Chain A, Solution Structure Of Chromo Domain 2 In Chromodomain-
Helicase-Dna-Binding Protein 6
Length = 68
Score = 30.4 bits (67), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 17/57 (29%), Positives = 29/57 (50%), Gaps = 2/57 (3%)
Query: 352 PGEYEVARIVDICYGDPNESGKRGLNFKVHWKGYSTSEDSWEPIEGLRNCPERIKEF 408
P EV RI+++ + E+G+ ++ V W E +WE E + P ++KEF
Sbjct: 9 PDYVEVDRILEVAHTKDAETGEEVTHYLVKWCSLPYEESTWELEEDVD--PAKVKEF 63
>pdb|3MTS|A Chain A, Chromo Domain Of Human Histone-lysine N-methyltransferase
Suv39h1
pdb|3MTS|B Chain B, Chromo Domain Of Human Histone-lysine N-methyltransferase
Suv39h1
pdb|3MTS|C Chain C, Chromo Domain Of Human Histone-lysine N-methyltransferase
Suv39h1
Length = 64
Score = 30.4 bits (67), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 13/34 (38%), Positives = 22/34 (64%), Gaps = 1/34 (2%)
Query: 378 FKVHWKGYSTSEDSWEPIEGLRNCPERIKEFVRN 411
+ V W+GY SE +WEP + L+ C +K+F ++
Sbjct: 18 YLVKWRGYPDSESTWEPRQNLK-CVRILKQFHKD 50
>pdb|3ME5|A Chain A, Crystal Structure Of Putative Dna Cytosine Methylase From
Shigella Flexneri 2a Str. 2457t
Length = 482
Score = 30.0 bits (66), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 27/110 (24%), Positives = 45/110 (40%), Gaps = 13/110 (11%)
Query: 425 DVICGGPPCQ--GISGYNRFRNVDSPLDDERNRQIVIFMDIVEFL---KPKYVLMENVVD 479
DV+ G PCQ ++G ++ ++ + Q +F D+V + +P ++ENV +
Sbjct: 171 DVLLAGFPCQPFSLAGVSKKNSLGRAHGFACDTQGTLFFDVVRIIDARRPAXFVLENVKN 230
Query: 480 ILKFDKASLGRYALSRLVHMKYQARFG--------IIAAGCYGLPQFRLR 521
+ DK R L + Y I G + LPQ R R
Sbjct: 231 LKSHDKGKTFRIIXQTLDELGYDVADAEDNGPDDPKIIDGKHFLPQHRER 280
>pdb|2J04|B Chain B, The Tau60-Tau91 Subcomplex Of Yeast Transcription Factor
Iiic
pdb|2J04|D Chain D, The Tau60-Tau91 Subcomplex Of Yeast Transcription Factor
Iiic
Length = 524
Score = 29.6 bits (65), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 28/65 (43%), Gaps = 6/65 (9%)
Query: 383 KGYSTSEDSWEPIEGLRNCPERIKEFVRNGFKSKILPLP------GDVDVICGGPPCQGI 436
K S++ D E I GL + V+ GF++ + P +C PPC+
Sbjct: 5 KDLSSARDKIERIYGLNKEKLLLLAKVKEGFETSVFDFPFKNIQPDSPYFVCLDPPCKKE 64
Query: 437 SGYNR 441
S YN+
Sbjct: 65 SAYNK 69
>pdb|3JXE|A Chain A, Crystal Structure Of Pyrococcus Horikoshii
Tryptophanyl-Trna Synthetase In Complex With Trpamp
pdb|3JXE|B Chain B, Crystal Structure Of Pyrococcus Horikoshii
Tryptophanyl-Trna Synthetase In Complex With Trpamp
Length = 392
Score = 29.6 bits (65), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 24/88 (27%), Positives = 36/88 (40%), Gaps = 3/88 (3%)
Query: 62 KGEGTQKHIGKILEFFKTTDGEEYFRVQWFYRAEDT---VMKEAADFHDRKRLFYSTVMN 118
+G HIG I+ FF T +E F V + + D + KE F D KR Y +++
Sbjct: 80 RGPSGPMHIGHIIPFFATKWLQEKFGVNLYIQITDDEKFLFKENLTFDDTKRWAYDNILD 139
Query: 119 DNPVDCIISKVIVAQIPPKIGLKSNSIP 146
V K + Q + +IP
Sbjct: 140 IIAVGFDPDKTFIFQNSEFTKIYEMAIP 167
>pdb|3LX6|A Chain A, Crystal Structure Of Putative Dna Cytosine Methylase From
Shigella Flexneri 2a Str. 2457t
pdb|3LX6|B Chain B, Crystal Structure Of Putative Dna Cytosine Methylase From
Shigella Flexneri 2a Str. 2457t
Length = 410
Score = 29.3 bits (64), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 27/110 (24%), Positives = 45/110 (40%), Gaps = 13/110 (11%)
Query: 425 DVICGGPPCQ--GISGYNRFRNVDSPLDDERNRQIVIFMDIVEFL---KPKYVLMENVVD 479
DV+ G PCQ ++G ++ ++ + Q +F D+V + +P ++ENV +
Sbjct: 109 DVLLAGFPCQPFSLAGVSKKNSLGRAHGFACDTQGTLFFDVVRIIDARRPAXFVLENVKN 168
Query: 480 ILKFDKASLGRYALSRLVHMKYQARFG--------IIAAGCYGLPQFRLR 521
+ DK R L + Y I G + LPQ R R
Sbjct: 169 LKSHDKGKTFRIIXQTLDELGYDVADAEDNGPDDPKIIDGKHFLPQHRER 218
>pdb|2RSN|A Chain A, Solution Structure Of The Chromodomain Of Chp1 In Complex
With H3k9me3 Peptide
Length = 75
Score = 28.5 bits (62), Expect = 9.3, Method: Composition-based stats.
Identities = 20/64 (31%), Positives = 30/64 (46%), Gaps = 12/64 (18%)
Query: 341 SVNSPRDVDIPPGE-----YEVARIVDICYGDPNESGKRGLN-FKVHWKGYSTSEDSWEP 394
SV D+D GE YEV I+ + K G+N + + W GY +++WEP
Sbjct: 3 SVKPLPDIDSNEGETDADVYEVEDIL------ADRVNKNGINEYYIKWAGYDWYDNTWEP 56
Query: 395 IEGL 398
+ L
Sbjct: 57 EQNL 60
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.319 0.136 0.419
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 15,569,274
Number of Sequences: 62578
Number of extensions: 667948
Number of successful extensions: 1484
Number of sequences better than 100.0: 57
Number of HSP's better than 100.0 without gapping: 30
Number of HSP's successfully gapped in prelim test: 27
Number of HSP's that attempted gapping in prelim test: 1396
Number of HSP's gapped (non-prelim): 76
length of query: 521
length of database: 14,973,337
effective HSP length: 103
effective length of query: 418
effective length of database: 8,527,803
effective search space: 3564621654
effective search space used: 3564621654
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 54 (25.4 bits)