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= psy10545
(1428 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4DGK|A Chain A, Crystal Structure Of Phytoene Desaturase Crti From Pantoea
Ananatis
Length = 501
Score = 531 bits (1368), Expect = e-150, Method: Compositional matrix adjust.
Identities = 246/473 (52%), Positives = 330/473 (69%), Gaps = 1/473 (0%)
Query: 729 RLQTAGISTIILEQRDKPGGRAYVYKQDGFIFDAGPTVITDPNSIKLLFDLSKNRMENYV 788
RLQ AGI ++LEQRDKPGGRAYVY+ GF FDAGPTVITDP++I+ LF L+ +++ YV
Sbjct: 19 RLQAAGIPVLLLEQRDKPGGRAYVYEDQGFTFDAGPTVITDPSAIEELFALAGKQLKEYV 78
Query: 789 NLLPIKPFYRLYWGKEKFLNYEDNIKDLEKQIAKFNLNDIKGYRLFLNYSKKVFKEGYLS 848
LLP+ PFYRL W K NY+++ LE QI +FN D++GYR FL+YS+ VFKEGYL
Sbjct: 79 ELLPVTPFYRLCWESGKVFNYDNDQTRLEAQIQQFNPRDVEGYRQFLDYSRAVFKEGYLK 138
Query: 849 FASKSFLTINDMLFILPKLIKIKAWKSVYSIVSQFIKNDYLKQAFSFNSLFIGGNPFSTS 908
+ FL+ DML P+L K++AW+SVYS V+ +I++++L+QAFSF+SL +GGNPF+TS
Sbjct: 139 LGTVPFLSFRDMLRAAPQLAKLQAWRSVYSKVASYIEDEHLRQAFSFHSLLVGGNPFATS 198
Query: 909 SIYTLIHALEYEWGIWFPKGGVGALIKALIKLFQNLGGNLILNSQVISIYXXXXXXXXXX 968
SIYTLIHALE EWG+WFP+GG GAL++ +IKLFQ+LGG ++LN++V +
Sbjct: 199 SIYTLIHALEREWGVWFPRGGTGALVQGMIKLFQDLGGEVVLNARVSHMETTGNKIEAVH 258
Query: 969 XXXGQIFDADIIVSNADIINTYRNLLGQYAFGXXXXXXXXXXXMSNSLFVIYFGLSEQYT 1028
G+ F + SNAD+++TYR+LL Q+ MSNSLFV+YFGL+ +
Sbjct: 259 LEDGRRFLTQAVASNADVVHTYRDLLSQHPAAVKQSNKLQTKRMSNSLFVLYFGLNHHHD 318
Query: 1029 HLAHHTIFFPSNYKKSIENIFGKNFSRDNLSIYLHSPSVTDLSLAPTGCSTFYALIPVPN 1088
LAHHT+ F Y++ I+ IF + ++ S+YLH+P VTD SLAP GC ++Y L PVP+
Sbjct: 319 QLAHHTVCFGPRYRELIDEIFNHDGLAEDFSLYLHAPCVTDSSLAPEGCGSYYVLAPVPH 378
Query: 1089 LXXXXXXXXXXXXKLKNIVFMYLEQYCIPNLRKKLITQRIFTPNDFKDVLGSYLGSAFSF 1148
L KL++ +F YLEQ+ +P LR +L+T R+FTP DF+D L +Y GSAFS
Sbjct: 379 LGTANLDWTVEGPKLRDRIFAYLEQHYMPGLRSQLVTHRMFTPFDFRDQLNAYHGSAFSV 438
Query: 1149 APLLTQSAWFRPHNRDKNLTNLYFVGAGTHPGAANKIIKAGSKSFSSAIKLFD 1201
P+LTQSAWFRPHNRDK +TNLY VGAGTHPGA + GS ++ + L D
Sbjct: 439 EPVLTQSAWFRPHNRDKTITNLYLVGAGTHPGAGIPGV-IGSAKATAGLMLED 490
>pdb|3VJD|A Chain A, Crystal Structure Of The Y248a Mutant Of C(30) Carotenoid
Dehydrosqualene Synthase From Staphylococcus Aureus
pdb|3VJE|A Chain A, Crystal Structure Of The Y248a Mutant Of C(30) Carotenoid
Dehydrosqualene Synthase From Staphylococcus Aureus In
Complex With Zaragozic Acid A
pdb|3VJE|B Chain B, Crystal Structure Of The Y248a Mutant Of C(30) Carotenoid
Dehydrosqualene Synthase From Staphylococcus Aureus In
Complex With Zaragozic Acid A
Length = 293
Score = 69.3 bits (168), Expect = 1e-11, Method: Composition-based stats.
Identities = 59/188 (31%), Positives = 78/188 (41%), Gaps = 24/188 (12%)
Query: 1183 NKIIKAGSKSFSSAIKLFDPVIRYKVLMLYAWCRYCDDVID--------NQICGNRSKFL 1234
+KI+K SKSFS A L R V +YA CR DD ID NQI +
Sbjct: 18 HKIMKKHSKSFSYAFDLLPEDQRKAVWAIYAVCRKIDDSIDVYGDIQFLNQIKEDIQSIE 77
Query: 1235 KKNVSMKHKLKILRIKTKRACIGFKMKEPAFLALQKIISIHSFPVHLLFEHLDGFEMDVM 1294
K H F+ +ALQ + + + +D D
Sbjct: 78 KYPYEYHH---------------FQSDRRIMMALQHVAQHKNIAFQSFYNLIDTVYKDQH 122
Query: 1295 ERTYITLDETLGYCYHVAGTIGLIIAHLIGVKEK-DTLNCARNLGIAFQLTNISRDVIDD 1353
+ T E GYCY VAGT+G ++ ++ E T + AR LG + QL NI RDV +D
Sbjct: 123 FTMFETDAELFGYCYGVAGTVGEVLTPILSDHETHQTYDVARRLGESLQLINILRDVGED 182
Query: 1354 FYVGRCYL 1361
F R Y
Sbjct: 183 FENERIYF 190
>pdb|2ZCO|A Chain A, Crystal Structure Of The C(30) Carotenoid Dehydrosqualene
Synthase From Staphylococcus Aureus
pdb|2ZCP|A Chain A, Crystal Structure Of The C(30) Carotenoid Dehydrosqualene
Synthase From Staphylococcus Aureus Complexed With
Farnesyl Thiopyrophosphate
pdb|2ZCP|B Chain B, Crystal Structure Of The C(30) Carotenoid Dehydrosqualene
Synthase From Staphylococcus Aureus Complexed With
Farnesyl Thiopyrophosphate
pdb|2ZCQ|A Chain A, Crystal Structure Of The C(30) Carotenoid Dehydrosqualene
Synthase From Staphylococcus Aureus Complexed With
Bisphosphonate Bph-652
pdb|2ZCR|A Chain A, Crystal Structure Of The C(30) Carotenoid Dehydrosqualene
Synthase From Staphylococcus Aureus Complexed With
Bisphosphonate Bph-698
pdb|2ZCS|A Chain A, Crystal Structure Of The C(30) Carotenoid Dehydrosqualene
Synthase From Staphylococcus Aureus Complexed With
Bisphosphonate Bph-700
pdb|2ZY1|A Chain A, Crystal Structure Of The C(30) Carotenoid Dehydrosqualene
Synthase From Staphylococcus Aureus Complexed With
Bisphosphonate Bph-830
pdb|3ACW|A Chain A, Crystal Structure Of The C(30) Carotenoid Dehydrosqualene
Synthase From Staphylococcus Aureus Complexed With
Bph-651
pdb|3ACX|A Chain A, Crystal Structure Of The C(30) Carotenoid Dehydrosqualene
Synthase From Staphylococcus Aureus Complexed With
Bph-673
pdb|3ACY|A Chain A, Crystal Structure Of The C(30) Carotenoid Dehydrosqualene
Synthase From Staphylococcus Aureus Complexed With
Bph-702
pdb|3NPR|A Chain A, Crystal Structure Of The C(30) Carotenoid Dehydrosqualene
Synthase From S. Aureus Complexed With Presqualene
Diphosphate (Pspp)
pdb|3NRI|A Chain A, Crystal Structure Of The C(30) Carotenoid Dehydrosqualene
Synthase From S. Aureus Complexed With Dehydrosqualene
(Dhs)
pdb|3TFN|A Chain A, Crystal Structure Of Dehydrosqualene Synthase (Crtm) From S.
Aureus Complexed With Bph-1183
pdb|3TFP|A Chain A, Crystal Structure Of Dehydrosqualene Synthase (Crtm) From S.
Aureus Complexed With Bph-1162
pdb|3TFV|A Chain A, Crystal Structure Of Dehydrosqualene Synthase (Crtm) From S.
Aureus Complexed With Bph-1154
Length = 293
Score = 69.3 bits (168), Expect = 2e-11, Method: Composition-based stats.
Identities = 59/188 (31%), Positives = 78/188 (41%), Gaps = 24/188 (12%)
Query: 1183 NKIIKAGSKSFSSAIKLFDPVIRYKVLMLYAWCRYCDDVID--------NQICGNRSKFL 1234
+KI+K SKSFS A L R V +YA CR DD ID NQI +
Sbjct: 18 HKIMKKHSKSFSYAFDLLPEDQRKAVWAIYAVCRKIDDSIDVYGDIQFLNQIKEDIQSIE 77
Query: 1235 KKNVSMKHKLKILRIKTKRACIGFKMKEPAFLALQKIISIHSFPVHLLFEHLDGFEMDVM 1294
K H F+ +ALQ + + + +D D
Sbjct: 78 KYPYEYHH---------------FQSDRRIMMALQHVAQHKNIAFQSFYNLIDTVYKDQH 122
Query: 1295 ERTYITLDETLGYCYHVAGTIGLIIAHLIGVKEK-DTLNCARNLGIAFQLTNISRDVIDD 1353
+ T E GYCY VAGT+G ++ ++ E T + AR LG + QL NI RDV +D
Sbjct: 123 FTMFETDAELFGYCYGVAGTVGEVLTPILSDHETHQTYDVARRLGESLQLINILRDVGED 182
Query: 1354 FYVGRCYL 1361
F R Y
Sbjct: 183 FENERIYF 190
>pdb|4E9U|A Chain A, Crystal Structure Of Dehydrosqualene Synthase (Crtm) From S.
Aureus Complexed With A Thiocyanate Inhibitor
pdb|4E9Z|A Chain A, Crystal Structure Of Dehydrosqualene Synthase (Crtm) From S.
Aureus Complexed With Quinuclidine Bph-651 In The S1 Site
pdb|4EA0|A Chain A, Crystal Structure Of Dehydrosqualene Synthase (Crtm) From S.
Aureus Complexed With Diphosphate And Quinuclidine
Bph-651
pdb|4EA0|B Chain B, Crystal Structure Of Dehydrosqualene Synthase (Crtm) From S.
Aureus Complexed With Diphosphate And Quinuclidine
Bph-651
pdb|4EA1|A Chain A, Co-Crystal Structure Of Dehydrosqualene Synthase (Crtm) From
S. Aureus With Sq-109
pdb|4EA2|A Chain A, Crystal Structure Of Dehydrosqualene Synthase (Crtm) Aureus
Complexed With Sq-109
Length = 287
Score = 69.3 bits (168), Expect = 2e-11, Method: Composition-based stats.
Identities = 59/188 (31%), Positives = 78/188 (41%), Gaps = 24/188 (12%)
Query: 1183 NKIIKAGSKSFSSAIKLFDPVIRYKVLMLYAWCRYCDDVID--------NQICGNRSKFL 1234
+KI+K SKSFS A L R V +YA CR DD ID NQI +
Sbjct: 12 HKIMKKHSKSFSYAFDLLPEDQRKAVWAIYAVCRKIDDSIDVYGDIQFLNQIKEDIQSIE 71
Query: 1235 KKNVSMKHKLKILRIKTKRACIGFKMKEPAFLALQKIISIHSFPVHLLFEHLDGFEMDVM 1294
K H F+ +ALQ + + + +D D
Sbjct: 72 KYPYEYHH---------------FQSDRRIMMALQHVAQHKNIAFQSFYNLIDTVYKDQH 116
Query: 1295 ERTYITLDETLGYCYHVAGTIGLIIAHLIGVKEK-DTLNCARNLGIAFQLTNISRDVIDD 1353
+ T E GYCY VAGT+G ++ ++ E T + AR LG + QL NI RDV +D
Sbjct: 117 FTMFETDAELFGYCYGVAGTVGEVLTPILSDHETHQTYDVARRLGESLQLINILRDVGED 176
Query: 1354 FYVGRCYL 1361
F R Y
Sbjct: 177 FENERIYF 184
>pdb|4F6V|A Chain A, Crystal Structure Of Dehydrosqualene Synthase (Crtm) From S.
Aureus Complexed With Bph-1034, Mg2+ And Fmp.
pdb|4F6X|A Chain A, Crystal Structure Of Dehydrosqualene Synthase (Crtm) From S.
Aureus Complexed With Bph-1112
Length = 292
Score = 68.9 bits (167), Expect = 2e-11, Method: Composition-based stats.
Identities = 59/188 (31%), Positives = 78/188 (41%), Gaps = 24/188 (12%)
Query: 1183 NKIIKAGSKSFSSAIKLFDPVIRYKVLMLYAWCRYCDDVID--------NQICGNRSKFL 1234
+KI+K SKSFS A L R V +YA CR DD ID NQI +
Sbjct: 17 HKIMKKHSKSFSYAFDLLPEDQRKAVWAIYAVCRKIDDSIDVYGDIQFLNQIKEDIQSIE 76
Query: 1235 KKNVSMKHKLKILRIKTKRACIGFKMKEPAFLALQKIISIHSFPVHLLFEHLDGFEMDVM 1294
K H F+ +ALQ + + + +D D
Sbjct: 77 KYPYEYHH---------------FQSDRRIMMALQHVAQHKNIAFQSFYNLIDTVYKDQH 121
Query: 1295 ERTYITLDETLGYCYHVAGTIGLIIAHLIGVKEK-DTLNCARNLGIAFQLTNISRDVIDD 1353
+ T E GYCY VAGT+G ++ ++ E T + AR LG + QL NI RDV +D
Sbjct: 122 FTMFETDAELFGYCYGVAGTVGEVLTPILSDHETHQTYDVARRLGESLQLINILRDVGED 181
Query: 1354 FYVGRCYL 1361
F R Y
Sbjct: 182 FENERIYF 189
>pdb|3AE0|A Chain A, Crystal Structure Of The C(30) Carotenoid Dehydrosqualene
Synthase From Staphylococcus Aureus Complexed With
Geranylgeranyl Thiopyrophosphate
pdb|3AE0|B Chain B, Crystal Structure Of The C(30) Carotenoid Dehydrosqualene
Synthase From Staphylococcus Aureus Complexed With
Geranylgeranyl Thiopyrophosphate
Length = 293
Score = 68.9 bits (167), Expect = 2e-11, Method: Composition-based stats.
Identities = 59/188 (31%), Positives = 78/188 (41%), Gaps = 24/188 (12%)
Query: 1183 NKIIKAGSKSFSSAIKLFDPVIRYKVLMLYAWCRYCDDVID--------NQICGNRSKFL 1234
+KI+K SKSFS A L R V +YA CR DD ID NQI +
Sbjct: 18 HKIMKKHSKSFSYAADLLPEDQRKAVWAIYAVCRKIDDSIDVYGDIQFLNQIKEDIQSIE 77
Query: 1235 KKNVSMKHKLKILRIKTKRACIGFKMKEPAFLALQKIISIHSFPVHLLFEHLDGFEMDVM 1294
K H F+ +ALQ + + + +D D
Sbjct: 78 KYPYEYHH---------------FQSDRRIMMALQHVAQHKNIAFQSFYNLIDTVYKDQH 122
Query: 1295 ERTYITLDETLGYCYHVAGTIGLIIAHLIGVKEK-DTLNCARNLGIAFQLTNISRDVIDD 1353
+ T E GYCY VAGT+G ++ ++ E T + AR LG + QL NI RDV +D
Sbjct: 123 FTMFETDAELFGYCYGVAGTVGEVLTPILSDHETHQTYDVARRLGESLQLINILRDVGED 182
Query: 1354 FYVGRCYL 1361
F R Y
Sbjct: 183 FENERIYF 190
>pdb|3ADZ|A Chain A, Crystal Structure Of The C(30) Carotenoid Dehydrosqualene
Synthase From Staphylococcus Aureus Complexed With
Intermediate Pspp
pdb|3LGZ|B Chain B, Crystal Structure Of Dehydrosqualene Synthase Y129a From S.
Aureus Complexed With Presqualene Pyrophosphate
Length = 293
Score = 65.9 bits (159), Expect = 1e-10, Method: Composition-based stats.
Identities = 58/188 (30%), Positives = 77/188 (40%), Gaps = 24/188 (12%)
Query: 1183 NKIIKAGSKSFSSAIKLFDPVIRYKVLMLYAWCRYCDDVID--------NQICGNRSKFL 1234
+KI+K SKSFS A L R V +YA CR DD ID NQI +
Sbjct: 18 HKIMKKHSKSFSYAFDLLPEDQRKAVWAIYAVCRKIDDSIDVYGDIQFLNQIKEDIQSIE 77
Query: 1235 KKNVSMKHKLKILRIKTKRACIGFKMKEPAFLALQKIISIHSFPVHLLFEHLDGFEMDVM 1294
K H F+ +ALQ + + + +D D
Sbjct: 78 KYPYEYHH---------------FQSDRRIMMALQHVAQHKNIAFQSFYNLIDTVYKDQH 122
Query: 1295 ERTYITLDETLGYCYHVAGTIGLIIAHLIGVKEK-DTLNCARNLGIAFQLTNISRDVIDD 1353
+ T E G CY VAGT+G ++ ++ E T + AR LG + QL NI RDV +D
Sbjct: 123 FTMFETDAELFGACYGVAGTVGEVLTPILSDHETHQTYDVARRLGESLQLINILRDVGED 182
Query: 1354 FYVGRCYL 1361
F R Y
Sbjct: 183 FENERIYF 190
>pdb|4HD1|A Chain A, Crystal Structure Of Squalene Synthase Hpnc From
Alicyclobacillus Acidocaldarius
Length = 294
Score = 57.0 bits (136), Expect = 7e-08, Method: Composition-based stats.
Identities = 44/169 (26%), Positives = 74/169 (43%), Gaps = 13/169 (7%)
Query: 1195 SAIKLFDPV-IRYKVLMLYAWCRYCDDVIDNQICGNRSKFLKKNVSMKHKLKILRIKTKR 1253
S + LF P +R +YA+CR DD+ D + G+R L + +R
Sbjct: 30 SVVSLFVPRHLRPHFYSVYAFCRGVDDLGD-EFAGDRXA----------ALDAYEEELRR 78
Query: 1254 ACIGFKMKEPAFLALQKIISIHSFPVHLLFEHLDGFEMDVMERTYITLDETLGYCYHVAG 1313
A G + PAF ALQ I+ + P ++ D + TY T ++ YC + A
Sbjct: 79 AFAG-EATTPAFRALQFTIATCNLPXEPFLRLIEANRRDQRKHTYDTWEDLRDYCRYSAD 137
Query: 1314 TIGLIIAHLIGVKEKDTLNCARNLGIAFQLTNISRDVIDDFYVGRCYLP 1362
+G ++ + G + + + A Q+ N +D+ D +GR Y+P
Sbjct: 138 PVGRLVLGIFGCLDDERARLSDATCTALQVANHXQDIDRDLALGRIYVP 186
>pdb|1EZF|A Chain A, Crystal Structure Of Human Squalene Synthase
pdb|1EZF|B Chain B, Crystal Structure Of Human Squalene Synthase
pdb|1EZF|C Chain C, Crystal Structure Of Human Squalene Synthase
Length = 340
Score = 45.4 bits (106), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 51/203 (25%), Positives = 83/203 (40%), Gaps = 28/203 (13%)
Query: 1184 KIIKAGSKSFSSAIKLFDPVIRYKVLMLYAWCRYCDDVIDNQICGNRSKFLKKNVSMKHK 1243
K + S+SF++ I+ D +R V + Y R D + D+ ++K V + H
Sbjct: 15 KYLNQTSRSFAAVIQALDGEMRNAVCIFYLVLRALDTLEDDMTIS-----VEKKVPLLHN 69
Query: 1244 LKILRIKTKRACIGFKMKEPAFLALQKIISIHSFPVHLLFEHLDGFEMDVMERTYITLDE 1303
+ + K K+ L IS+ L E D+ R I + E
Sbjct: 70 FHSFLYQPDWRFMESKEKDRQVLEDFPTISLE---FRNLAEKYQTVIADICRRMGIGMAE 126
Query: 1304 TLG-----------YCYHVAGTIGLIIAHLIGVKE-------KDTLNCARNLGIAFQLTN 1345
L YC++VAG +G+ ++ L E +DT A ++G+ Q TN
Sbjct: 127 FLDKHVTSEQEWDKYCHYVAGLVGIGLSRLFSASEFEDPLVGEDTER-ANSMGLFLQKTN 185
Query: 1346 ISRDVIDDFYVGRCYLPLD-WLR 1367
I RD ++D GR + P + W R
Sbjct: 186 IIRDYLEDQQGGREFWPQEVWSR 208
>pdb|3LEE|A Chain A, Crystal Structure Of The Human Squalene Synthase Complexed
With Bph- 652
pdb|3LEE|B Chain B, Crystal Structure Of The Human Squalene Synthase Complexed
With Bph- 652
pdb|3LEE|C Chain C, Crystal Structure Of The Human Squalene Synthase Complexed
With Bph- 652
pdb|3LEE|D Chain D, Crystal Structure Of The Human Squalene Synthase Complexed
With Bph- 652
pdb|3LEE|E Chain E, Crystal Structure Of The Human Squalene Synthase Complexed
With Bph- 652
pdb|3LEE|F Chain F, Crystal Structure Of The Human Squalene Synthase Complexed
With Bph- 652
pdb|3ASX|A Chain A, Human Squalene Synthase In Complex With
1-{4-[{4-Chloro-2-[(2-
Chlorophenyl)(Hydroxy)methyl]phenyl}(2,
2-Dimethylpropyl)amino]-4-
Oxobutanoyl}piperidine-3-Carboxylic Acid
pdb|3Q2Z|A Chain A, Human Squalene Synthase In Complex With
N-[(3r,5s)-7-Chloro-5-(2,3-
Dimethoxyphenyl)-1-Neopentyl-2-Oxo-1,2,3,5-Tetrahydro-4,
1- Benzoxazepine-3-Acetyl]-L-Aspartic Acid
pdb|3Q30|A Chain A, Human Squalene Synthase In Complex With
(2r,3r)-2-Carboxymethoxy-3-[5-
(2-Naphthalenyl)pentyl]aminocarbonyl-3-[5-(2-
Naphthalenyl) Pentyloxy]propionic Acid
pdb|3V66|A Chain A, Human Squalene Synthase In Complex With
2-(1-{2-[(4r,6s)-8-Chloro-6-
(2,3-Dimethoxyphenyl)-4h,6h-Pyrrolo[1,2-A][4,
1]benzoxazepin-4- Yl]acetyl}-4-Piperidinyl)acetic Acid
Length = 340
Score = 45.4 bits (106), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 51/203 (25%), Positives = 83/203 (40%), Gaps = 28/203 (13%)
Query: 1184 KIIKAGSKSFSSAIKLFDPVIRYKVLMLYAWCRYCDDVIDNQICGNRSKFLKKNVSMKHK 1243
K + S+SF++ I+ D +R V + Y R D + D+ ++K V + H
Sbjct: 15 KYLNQTSRSFAAVIQALDGEMRNAVCIFYLVLRALDTLEDDMTIS-----VEKKVPLLHN 69
Query: 1244 LKILRIKTKRACIGFKMKEPAFLALQKIISIHSFPVHLLFEHLDGFEMDVMERTYITLDE 1303
+ + K K+ L IS+ L E D+ R I + E
Sbjct: 70 FHSFLYQPDWRFMESKEKDRQVLEDFPTISLE---FRNLAEKYQTVIADICRRMGIGMAE 126
Query: 1304 TLG-----------YCYHVAGTIGLIIAHLIGVKE-------KDTLNCARNLGIAFQLTN 1345
L YC++VAG +G+ ++ L E +DT A ++G+ Q TN
Sbjct: 127 FLDKHVTSEQEWDKYCHYVAGLVGIGLSRLFSASEFEDPLVGEDTER-ANSMGLFLQKTN 185
Query: 1346 ISRDVIDDFYVGRCYLPLD-WLR 1367
I RD ++D GR + P + W R
Sbjct: 186 IIRDYLEDQQGGREFWPQEVWSR 208
>pdb|3VJ8|A Chain A, Crystal Structure Of The Human Squalene Synthase
pdb|3VJ9|A Chain A, Crystal Structure Of The Human Squalene Synthase
pdb|3VJA|A Chain A, Crystal Structure Of The Human Squalene Synthase
pdb|3VJA|B Chain B, Crystal Structure Of The Human Squalene Synthase
pdb|3VJB|A Chain A, Crystal Structure Of The Human Squalene Synthase
pdb|3VJB|B Chain B, Crystal Structure Of The Human Squalene Synthase
pdb|3VJB|C Chain C, Crystal Structure Of The Human Squalene Synthase
pdb|3VJB|D Chain D, Crystal Structure Of The Human Squalene Synthase
pdb|3VJB|E Chain E, Crystal Structure Of The Human Squalene Synthase
pdb|3VJB|F Chain F, Crystal Structure Of The Human Squalene Synthase
pdb|3VJC|A Chain A, Crystal Structure Of The Human Squalene Synthase In Complex
With Zaragozic Acid A
pdb|3VJC|B Chain B, Crystal Structure Of The Human Squalene Synthase In Complex
With Zaragozic Acid A
pdb|3VJC|C Chain C, Crystal Structure Of The Human Squalene Synthase In Complex
With Zaragozic Acid A
pdb|3VJC|D Chain D, Crystal Structure Of The Human Squalene Synthase In Complex
With Zaragozic Acid A
pdb|3VJC|E Chain E, Crystal Structure Of The Human Squalene Synthase In Complex
With Zaragozic Acid A
pdb|3VJC|F Chain F, Crystal Structure Of The Human Squalene Synthase In Complex
With Zaragozic Acid A
Length = 343
Score = 45.4 bits (106), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 51/203 (25%), Positives = 83/203 (40%), Gaps = 28/203 (13%)
Query: 1184 KIIKAGSKSFSSAIKLFDPVIRYKVLMLYAWCRYCDDVIDNQICGNRSKFLKKNVSMKHK 1243
K + S+SF++ I+ D +R V + Y R D + D+ ++K V + H
Sbjct: 18 KYLNQTSRSFAAVIQALDGEMRNAVCIFYLVLRALDTLEDDMTIS-----VEKKVPLLHN 72
Query: 1244 LKILRIKTKRACIGFKMKEPAFLALQKIISIHSFPVHLLFEHLDGFEMDVMERTYITLDE 1303
+ + K K+ L IS+ L E D+ R I + E
Sbjct: 73 FHSFLYQPDWRFMESKEKDRQVLEDFPTISLE---FRNLAEKYQTVIADICRRMGIGMAE 129
Query: 1304 TLG-----------YCYHVAGTIGLIIAHLIGVKE-------KDTLNCARNLGIAFQLTN 1345
L YC++VAG +G+ ++ L E +DT A ++G+ Q TN
Sbjct: 130 FLDKHVTSEQEWDKYCHYVAGLVGIGLSRLFSASEFEDPLVGEDTER-ANSMGLFLQKTN 188
Query: 1346 ISRDVIDDFYVGRCYLPLD-WLR 1367
I RD ++D GR + P + W R
Sbjct: 189 IIRDYLEDQQGGREFWPQEVWSR 211
>pdb|2HKO|A Chain A, Crystal Structure Of Lsd1
Length = 664
Score = 37.0 bits (84), Expect = 0.086, Method: Compositional matrix adjust.
Identities = 14/40 (35%), Positives = 25/40 (62%)
Query: 729 RLQTAGISTIILEQRDKPGGRAYVYKQDGFIFDAGPTVIT 768
+LQ+ G+ +LE RD+ GGR +++ ++ D G V+T
Sbjct: 125 QLQSFGMDVTLLEARDRVGGRVATFRKGNYVADLGAMVVT 164
>pdb|2H94|A Chain A, Crystal Structure And Mechanism Of Human Lysine-Specific
Demethylase-1
Length = 664
Score = 37.0 bits (84), Expect = 0.086, Method: Compositional matrix adjust.
Identities = 14/40 (35%), Positives = 25/40 (62%)
Query: 729 RLQTAGISTIILEQRDKPGGRAYVYKQDGFIFDAGPTVIT 768
+LQ+ G+ +LE RD+ GGR +++ ++ D G V+T
Sbjct: 125 QLQSFGMDVTLLEARDRVGGRVATFRKGNYVADLGAMVVT 164
>pdb|2EJR|A Chain A, Lsd1-Tranylcypromine Complex
pdb|2Z3Y|A Chain A, Crystal Structure Of Lysine-Specific Demethylase1
pdb|2Z5U|A Chain A, Crystal Structure Of Lysine-Specific Histone Demethylase 1
pdb|3ABT|A Chain A, Crystal Structure Of Lsd1 In Complex With Trans-2-
Pentafluorophenylcyclopropylamine
pdb|3ABU|A Chain A, Crystal Structure Of Lsd1 In Complex With A 2-Pcpa
Derivative, S1201
Length = 662
Score = 37.0 bits (84), Expect = 0.087, Method: Compositional matrix adjust.
Identities = 14/40 (35%), Positives = 25/40 (62%)
Query: 729 RLQTAGISTIILEQRDKPGGRAYVYKQDGFIFDAGPTVIT 768
+LQ+ G+ +LE RD+ GGR +++ ++ D G V+T
Sbjct: 125 QLQSFGMDVTLLEARDRVGGRVATFRKGNYVADLGAMVVT 164
>pdb|2DW4|A Chain A, Crystal Structure Of Human Lsd1 At 2.3 A Resolution
Length = 660
Score = 37.0 bits (84), Expect = 0.087, Method: Compositional matrix adjust.
Identities = 14/40 (35%), Positives = 25/40 (62%)
Query: 729 RLQTAGISTIILEQRDKPGGRAYVYKQDGFIFDAGPTVIT 768
+LQ+ G+ +LE RD+ GGR +++ ++ D G V+T
Sbjct: 125 QLQSFGMDVTLLEARDRVGGRVATFRKGNYVADLGAMVVT 164
>pdb|2IW5|A Chain A, Structural Basis For Corest-dependent Demethylation Of
Nucleosomes By The Human Lsd1 Histone Demethylase
pdb|2UXN|A Chain A, Structural Basis Of Histone Demethylation By Lsd1 Revealed
By Suicide Inactivation
pdb|2UXX|A Chain A, Human Lsd1 Histone Demethylase-Corest In Complex With An
Fad-Tranylcypromine Adduct
Length = 666
Score = 37.0 bits (84), Expect = 0.089, Method: Compositional matrix adjust.
Identities = 14/40 (35%), Positives = 25/40 (62%)
Query: 729 RLQTAGISTIILEQRDKPGGRAYVYKQDGFIFDAGPTVIT 768
+LQ+ G+ +LE RD+ GGR +++ ++ D G V+T
Sbjct: 126 QLQSFGMDVTLLEARDRVGGRVATFRKGNYVADLGAMVVT 165
>pdb|2X0L|A Chain A, Crystal Structure Of A Neuro-Specific Splicing Variant Of
Human Histone Lysine Demethylase Lsd1
Length = 734
Score = 36.6 bits (83), Expect = 0.092, Method: Compositional matrix adjust.
Identities = 14/40 (35%), Positives = 25/40 (62%)
Query: 729 RLQTAGISTIILEQRDKPGGRAYVYKQDGFIFDAGPTVIT 768
+LQ+ G+ +LE RD+ GGR +++ ++ D G V+T
Sbjct: 174 QLQSFGMDVTLLEARDRVGGRVATFRKGNYVADLGAMVVT 213
>pdb|2V1D|A Chain A, Structural Basis Of Lsd1-Corest Selectivity In Histone H3
Recognition
pdb|2Y48|A Chain A, Crystal Structure Of Lsd1-Corest In Complex With A N-
Terminal Snail Peptide
Length = 730
Score = 36.6 bits (83), Expect = 0.092, Method: Compositional matrix adjust.
Identities = 14/40 (35%), Positives = 25/40 (62%)
Query: 729 RLQTAGISTIILEQRDKPGGRAYVYKQDGFIFDAGPTVIT 768
+LQ+ G+ +LE RD+ GGR +++ ++ D G V+T
Sbjct: 174 QLQSFGMDVTLLEARDRVGGRVATFRKGNYVADLGAMVVT 213
>pdb|2VVL|G Chain G, The Structure Of Mao-N-D3, A Variant Of Monoamine Oxidase
From Aspergillus Niger
Length = 495
Score = 35.8 bits (81), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 15/38 (39%), Positives = 24/38 (63%)
Query: 730 LQTAGISTIILEQRDKPGGRAYVYKQDGFIFDAGPTVI 767
L AG T++LE RD+ GGR++ DG+ ++ G T +
Sbjct: 58 LTVAGFKTLLLEARDRIGGRSWSSNIDGYPYEMGGTWV 95
>pdb|2XAF|A Chain A, Crystal Structure Of Lsd1-Corest In Complex With
Para-Bromo- (+)-Cis-2-Phenylcyclopropyl-1-Amine
pdb|2XAG|A Chain A, Crystal Structure Of Lsd1-Corest In Complex With
Para-Bromo- (-)-Trans-2-Phenylcyclopropyl-1-Amine
pdb|2XAH|A Chain A, Crystal Structure Of Lsd1-Corest In Complex With (+)-
Trans-2-Phenylcyclopropyl-1-Amine
pdb|2XAJ|A Chain A, Crystal Structure Of Lsd1-Corest In Complex With
(-)-Trans- 2-Phenylcyclopropyl-1-Amine
pdb|2XAQ|A Chain A, Crystal Structure Of Lsd1-Corest In Complex With A
Tranylcypromine Derivative (Mc2584, 13b)
pdb|2XAS|A Chain A, Crystal Structure Of Lsd1-Corest In Complex With A
Tranylcypromine Derivative (Mc2580, 14e)
Length = 852
Score = 35.8 bits (81), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 14/40 (35%), Positives = 25/40 (62%)
Query: 729 RLQTAGISTIILEQRDKPGGRAYVYKQDGFIFDAGPTVIT 768
+LQ+ G+ +LE RD+ GGR +++ ++ D G V+T
Sbjct: 296 QLQSFGMDVTLLEARDRVGGRVATFRKGNYVADLGAMVVT 335
>pdb|2VVM|A Chain A, The Structure Of Mao-N-D5, A Variant Of Monoamine Oxidase
From Aspergillus Niger.
pdb|2VVM|B Chain B, The Structure Of Mao-N-D5, A Variant Of Monoamine Oxidase
From Aspergillus Niger
Length = 495
Score = 35.8 bits (81), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 15/38 (39%), Positives = 24/38 (63%)
Query: 730 LQTAGISTIILEQRDKPGGRAYVYKQDGFIFDAGPTVI 767
L AG T++LE RD+ GGR++ DG+ ++ G T +
Sbjct: 58 LTVAGFKTLLLEARDRIGGRSWSSNIDGYPYEMGGTWV 95
>pdb|2VVL|A Chain A, The Structure Of Mao-N-D3, A Variant Of Monoamine Oxidase
From Aspergillus Niger.
pdb|2VVL|B Chain B, The Structure Of Mao-N-D3, A Variant Of Monoamine Oxidase
From Aspergillus Niger.
pdb|2VVL|C Chain C, The Structure Of Mao-N-D3, A Variant Of Monoamine Oxidase
From Aspergillus Niger.
pdb|2VVL|D Chain D, The Structure Of Mao-N-D3, A Variant Of Monoamine Oxidase
From Aspergillus Niger.
pdb|2VVL|E Chain E, The Structure Of Mao-N-D3, A Variant Of Monoamine Oxidase
From Aspergillus Niger.
pdb|2VVL|F Chain F, The Structure Of Mao-N-D3, A Variant Of Monoamine Oxidase
From Aspergillus Niger.
pdb|2VVL|H Chain H, The Structure Of Mao-N-D3, A Variant Of Monoamine Oxidase
From Aspergillus Niger
Length = 495
Score = 35.8 bits (81), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 15/38 (39%), Positives = 24/38 (63%)
Query: 730 LQTAGISTIILEQRDKPGGRAYVYKQDGFIFDAGPTVI 767
L AG T++LE RD+ GGR++ DG+ ++ G T +
Sbjct: 58 LTVAGFKTLLLEARDRIGGRSWSSNIDGYPYEMGGTWV 95
>pdb|2YG7|A Chain A, Structure-Based Redesign Of Cofactor Binding In Putrescine
Oxidase: A394c-A396t-Q431g Triple Mutant
pdb|2YG7|B Chain B, Structure-Based Redesign Of Cofactor Binding In Putrescine
Oxidase: A394c-A396t-Q431g Triple Mutant
Length = 453
Score = 35.0 bits (79), Expect = 0.34, Method: Composition-based stats.
Identities = 19/60 (31%), Positives = 31/60 (51%), Gaps = 2/60 (3%)
Query: 730 LQTAGISTIILEQRDKPGGRAYVYKQDGFIFDAGPTVITDPNS--IKLLFDLSKNRMENY 787
L+ AG+S ++E RD+ GGR + DG + + G ++ + I LL +L E Y
Sbjct: 24 LRKAGLSVAVIEARDRVGGRTWTDTIDGAVLEIGGQWVSPDQTALISLLDELGLKTFERY 83
>pdb|2YG6|A Chain A, Structure-Based Redesign Of Cofactor Binding In Putrescine
Oxidase: P15i-A394c Double Mutant
pdb|2YG6|B Chain B, Structure-Based Redesign Of Cofactor Binding In Putrescine
Oxidase: P15i-A394c Double Mutant
Length = 453
Score = 35.0 bits (79), Expect = 0.34, Method: Composition-based stats.
Identities = 19/60 (31%), Positives = 31/60 (51%), Gaps = 2/60 (3%)
Query: 730 LQTAGISTIILEQRDKPGGRAYVYKQDGFIFDAGPTVITDPNS--IKLLFDLSKNRMENY 787
L+ AG+S ++E RD+ GGR + DG + + G ++ + I LL +L E Y
Sbjct: 24 LRKAGLSVAVIEARDRVGGRTWTDTIDGAVLEIGGQWVSPDQTALISLLDELGLKTFERY 83
>pdb|2YG5|A Chain A, Structure-Based Redesign Of Cofactor Binding In Putrescine
Oxidase: A394c Mutant
Length = 453
Score = 35.0 bits (79), Expect = 0.34, Method: Composition-based stats.
Identities = 19/60 (31%), Positives = 31/60 (51%), Gaps = 2/60 (3%)
Query: 730 LQTAGISTIILEQRDKPGGRAYVYKQDGFIFDAGPTVITDPNS--IKLLFDLSKNRMENY 787
L+ AG+S ++E RD+ GGR + DG + + G ++ + I LL +L E Y
Sbjct: 24 LRKAGLSVAVIEARDRVGGRTWTDTIDGAVLEIGGQWVSPDQTALISLLDELGLKTFERY 83
>pdb|2YG3|A Chain A, Structure-Based Redesign Of Cofactor Binding In Putrescine
Oxidase: Wild Type Enzyme
pdb|2YG3|B Chain B, Structure-Based Redesign Of Cofactor Binding In Putrescine
Oxidase: Wild Type Enzyme
pdb|2YG4|A Chain A, Structure-Based Redesign Of Cofactor Binding In Putrescine
Oxidase: Wild Type Bound To Putrescine
pdb|2YG4|B Chain B, Structure-Based Redesign Of Cofactor Binding In Putrescine
Oxidase: Wild Type Bound To Putrescine
Length = 453
Score = 35.0 bits (79), Expect = 0.34, Method: Composition-based stats.
Identities = 19/60 (31%), Positives = 31/60 (51%), Gaps = 2/60 (3%)
Query: 730 LQTAGISTIILEQRDKPGGRAYVYKQDGFIFDAGPTVITDPNS--IKLLFDLSKNRMENY 787
L+ AG+S ++E RD+ GGR + DG + + G ++ + I LL +L E Y
Sbjct: 24 LRKAGLSVAVIEARDRVGGRTWTDTIDGAVLEIGGQWVSPDQTALISLLDELGLKTFERY 83
>pdb|3RHA|A Chain A, The Crystal Structure Of Oxidoreductase From Arthrobacter
Aurescens
pdb|3RHA|B Chain B, The Crystal Structure Of Oxidoreductase From Arthrobacter
Aurescens
Length = 482
Score = 33.5 bits (75), Expect = 0.86, Method: Compositional matrix adjust.
Identities = 16/48 (33%), Positives = 27/48 (56%), Gaps = 1/48 (2%)
Query: 729 RLQTAGISTIILEQRDKPGGRAYVYKQDGFIFDAGPTVITDPNSIKLL 776
L+ AG+S +LE RD+ GGR + DG + + G ++ P+ L+
Sbjct: 25 ELKKAGLSVAVLEARDRVGGRTWTDTIDGAMLEIGGQWVS-PDQTVLM 71
>pdb|4A3C|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 5nt
Dna-Rna Hybrid
pdb|4A3B|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 4nt
Dna-Rna Hybrid
pdb|4A3D|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 6nt
Dna-Rna Hybrid
pdb|4A3E|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 5nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3F|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 6nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3J|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 2nt
Dna-Rna Hybrid And Soaked With Gmpcpp
pdb|4A3K|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 7nt
Dna-Rna Hybrid
pdb|4A3L|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 7nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3M|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 4nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3G|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 2nt
Dna-Rna Hybrid
pdb|4A3I|A Chain A, Rna Polymerase Ii Binary Complex With Dna
pdb|4A93|A Chain A, Rna Polymerase Ii Elongation Complex Containing A Cpd Lesion
Length = 1732
Score = 32.3 bits (72), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 33/113 (29%), Positives = 48/113 (42%), Gaps = 8/113 (7%)
Query: 1142 LGSAFSFAPLLTQSAWFRPHNRDKNLTNLYFVGAGTHPGAANKIIKAGSKSFSSAIKLFD 1201
+G S A LT P+N D+ LT L G HPGA I +G + I L
Sbjct: 364 VGVPKSIAKTLTYPEVVTPYNIDR-LTQLVRNGPNEHPGAKYVIRDSGDR-----IDLRY 417
Query: 1202 PVIRYKVLMLYAWCRYCDDVIDNQ-ICGNRSKFLKKNVSMKHKLKILRIKTKR 1253
+ + Y W + ++DN + NR L K M H++K++ T R
Sbjct: 418 SKRAGDIQLQYGW-KVERHIMDNDPVLFNRQPSLHKMSMMAHRVKVIPYSTFR 469
>pdb|1I3Q|A Chain A, Rna Polymerase Ii Crystal Form I At 3.1 A Resolution
pdb|1I50|A Chain A, Rna Polymerase Ii Crystal Form Ii At 2.8 A Resolution
pdb|1I6H|A Chain A, Rna Polymerase Ii Elongation Complex
pdb|1K83|A Chain A, Crystal Structure Of Yeast Rna Polymerase Ii Complexed With
The Inhibitor Alpha Amanitin
pdb|1NIK|A Chain A, Wild Type Rna Polymerase Ii
pdb|1NT9|A Chain A, Complete 12-Subunit Rna Polymerase Ii
pdb|1PQV|A Chain A, Rna Polymerase Ii-Tfiis Complex
pdb|1R5U|A Chain A, Rna Polymerase Ii Tfiib Complex
pdb|1SFO|A Chain A, Rna Polymerase Ii Strand Separated Elongation Complex
pdb|1R9S|A Chain A, Rna Polymerase Ii Strand Separated Elongation Complex,
Matched Nucleotide
pdb|1R9T|A Chain A, Rna Polymerase Ii Strand Separated Elongation Complex,
Mismatched Nucleotide
pdb|1TWA|A Chain A, Rna Polymerase Ii Complexed With Atp
pdb|1TWC|A Chain A, Rna Polymerase Ii Complexed With Gtp
pdb|1TWF|A Chain A, Rna Polymerase Ii Complexed With Utp At 2.3 A Resolution
pdb|1TWG|A Chain A, Rna Polymerase Ii Complexed With Ctp
pdb|1TWH|A Chain A, Rna Polymerase Ii Complexed With 2'datp
pdb|1WCM|A Chain A, Complete 12-Subunit Rna Polymerase Ii At 3.8 Ang
pdb|1Y1W|A Chain A, Complete Rna Polymerase Ii Elongation Complex
pdb|1Y77|A Chain A, Complete Rna Polymerase Ii Elongation Complex With Substrate
Analogue Gmpcpp
pdb|1Y1V|A Chain A, Refined Rna Polymerase Ii-tfiis Complex
pdb|1Y1Y|A Chain A, Rna Polymerase Ii-Tfiis-DnaRNA COMPLEX
pdb|2B63|A Chain A, Complete Rna Polymerase Ii-Rna Inhibitor Complex
pdb|2B8K|A Chain A, 12-Subunit Rna Polymerase Ii
pdb|2E2H|A Chain A, Rna Polymerase Ii Elongation Complex At 5 Mm Mg2+ With Gtp
pdb|2E2I|A Chain A, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With 2'-
Dgtp
pdb|2E2J|A Chain A, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With
Gmpcpp
pdb|2NVQ|A Chain A, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With
2'dutp
pdb|2NVT|A Chain A, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With
Gmpcpp
pdb|2NVX|A Chain A, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With 2'-
Dutp
pdb|2NVY|A Chain A, Rna Polymerase Ii Form Ii In 150 Mm Mn+2
pdb|2NVZ|A Chain A, Rna Polymerase Ii Elongation Complex With Utp, Updated
112006
pdb|2JA5|A Chain A, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex A
pdb|2JA6|A Chain A, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex B
pdb|2JA7|A Chain A, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex C
pdb|2JA7|M Chain M, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex C
pdb|2JA8|A Chain A, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex D
pdb|2YU9|A Chain A, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With Utp
pdb|2R7Z|A Chain A, Cisplatin Lesion Containing Rna Polymerase Ii Elongation
Complex
pdb|2R92|A Chain A, Elongation Complex Of Rna Polymerase Ii With Artificial Rdrp
Scaffold
pdb|2R93|A Chain A, Elongation Complex Of Rna Polymerase Ii With A Hepatitis
Delta Virus-Derived Rna Stem Loop
pdb|2VUM|A Chain A, Alpha-Amanitin Inhibited Complete Rna Polymerase Ii
Elongation Complex
pdb|3CQZ|A Chain A, Crystal Structure Of 10 Subunit Rna Polymerase Ii In Complex
With The Inhibitor Alpha-Amanitin
pdb|3FKI|A Chain A, 12-Subunit Rna Polymerase Ii Refined With Zn-Sad Data
pdb|3GTG|A Chain A, Backtracked Rna Polymerase Ii Complex With 12mer Rna
pdb|3GTJ|A Chain A, Backtracked Rna Polymerase Ii Complex With 13mer Rna
pdb|3GTK|A Chain A, Backtracked Rna Polymerase Ii Complex With 18mer Rna
pdb|3GTL|A Chain A, Backtracked Rna Polymerase Ii Complex With 13mer With G<>u
Mismatch
pdb|3GTM|A Chain A, Co-Complex Of Backtracked Rna Polymerase Ii With Tfiis
pdb|3GTO|A Chain A, Backtracked Rna Polymerase Ii Complex With 15mer Rna
pdb|3GTP|A Chain A, Backtracked Rna Polymerase Ii Complex With 24mer Rna
pdb|3GTQ|A Chain A, Backtracked Rna Polymerase Ii Complex Induced By Damage
pdb|3H3V|B Chain B, Yeast Rnap Ii Containing Poly(A)-Signal Sequence In The
Active Site
pdb|3HOU|A Chain A, Complete Rna Polymerase Ii Elongation Complex I With A T-U
Mismatch
pdb|3HOU|M Chain M, Complete Rna Polymerase Ii Elongation Complex I With A T-U
Mismatch
pdb|3HOV|A Chain A, Complete Rna Polymerase Ii Elongation Complex Ii
pdb|3HOW|A Chain A, Complete Rna Polymerase Ii Elongation Complex Iii With A T-U
Mismatch And A Frayed Rna 3'-Uridine
pdb|3HOX|A Chain A, Complete Rna Polymerase Ii Elongation Complex V
pdb|3HOY|A Chain A, Complete Rna Polymerase Ii Elongation Complex Vi
pdb|3HOZ|A Chain A, Complete Rna Polymerase Ii Elongation Complex Iv With A T-U
Mismatch And A Frayed Rna 3'-Guanine
pdb|3I4M|A Chain A, 8-oxoguanine Containing Rna Polymerase Ii Elongation Complex
D
pdb|3I4N|A Chain A, 8-oxoguanine Containing Rna Polymerase Ii Elongation Complex
E
pdb|3K1F|A Chain A, Crystal Structure Of Rna Polymerase Ii In Complex With Tfiib
pdb|3K7A|A Chain A, Crystal Structure Of An Rna Polymerase Ii-Tfiib Complex
pdb|3M3Y|A Chain A, Rna Polymerase Ii Elongation Complex C
pdb|3M4O|A Chain A, Rna Polymerase Ii Elongation Complex B
pdb|3PO2|A Chain A, Arrested Rna Polymerase Ii Elongation Complex
pdb|3PO3|A Chain A, Arrested Rna Polymerase Ii Reactivation Intermediate
pdb|3QT1|A Chain A, Rna Polymerase Ii Variant Containing A Chimeric Rpb9-C11
Subunit
pdb|3RZD|A Chain A, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
pdb|3RZO|A Chain A, Rna Polymerase Ii Initiation Complex With A 4-Nt Rna
pdb|3S14|A Chain A, Rna Polymerase Ii Initiation Complex With A 6-Nt Rna
pdb|3S15|A Chain A, Rna Polymerase Ii Initiation Complex With A 7-Nt Rna
pdb|3S16|A Chain A, Rna Polymerase Ii Initiation Complex With An 8-Nt Rna
pdb|3S17|A Chain A, Rna Polymerase Ii Initiation Complex With A 9-Nt Rna
pdb|3S1M|A Chain A, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
(Variant 1)
pdb|3S1N|A Chain A, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
(Variant 2)
pdb|3S1Q|A Chain A, Rna Polymerase Ii Initiation Complex With A 5-Nt 3'-Deoxy
Rna Soaked With Atp
pdb|3S1R|A Chain A, Rna Polymerase Ii Initiation Complex With A 5-Nt 3'-Deoxy
Rna Soaked With Gtp
pdb|3S2D|A Chain A, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
Containing A 5br- U
pdb|3S2H|A Chain A, Rna Polymerase Ii Initiation Complex With A 6-Nt Rna
Containing A 2[prime]-Iodo Atp
pdb|4BBR|A Chain A, Structure Of Rna Polymerase Ii-tfiib Complex
pdb|4BBS|A Chain A, Structure Of An Initially Transcribing Rna Polymerase Ii-
Tfiib Complex
Length = 1733
Score = 32.3 bits (72), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 33/113 (29%), Positives = 48/113 (42%), Gaps = 8/113 (7%)
Query: 1142 LGSAFSFAPLLTQSAWFRPHNRDKNLTNLYFVGAGTHPGAANKIIKAGSKSFSSAIKLFD 1201
+G S A LT P+N D+ LT L G HPGA I +G + I L
Sbjct: 364 VGVPKSIAKTLTYPEVVTPYNIDR-LTQLVRNGPNEHPGAKYVIRDSGDR-----IDLRY 417
Query: 1202 PVIRYKVLMLYAWCRYCDDVIDNQ-ICGNRSKFLKKNVSMKHKLKILRIKTKR 1253
+ + Y W + ++DN + NR L K M H++K++ T R
Sbjct: 418 SKRAGDIQLQYGW-KVERHIMDNDPVLFNRQPSLHKMSMMAHRVKVIPYSTFR 469
>pdb|3J0K|A Chain A, Orientation Of Rna Polymerase Ii Within The Human
Vp16-Mediator-Pol Ii-Tfiif Assembly
Length = 1455
Score = 32.3 bits (72), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 33/113 (29%), Positives = 48/113 (42%), Gaps = 8/113 (7%)
Query: 1142 LGSAFSFAPLLTQSAWFRPHNRDKNLTNLYFVGAGTHPGAANKIIKAGSKSFSSAIKLFD 1201
+G S A LT P+N D+ LT L G HPGA I +G + I L
Sbjct: 364 VGVPKSIAKTLTYPEVVTPYNIDR-LTQLVRNGPNEHPGAKYVIRDSGDR-----IDLRY 417
Query: 1202 PVIRYKVLMLYAWCRYCDDVIDNQ-ICGNRSKFLKKNVSMKHKLKILRIKTKR 1253
+ + Y W + ++DN + NR L K M H++K++ T R
Sbjct: 418 SKRAGDIQLQYGW-KVERHIMDNDPVLFNRQPSLHKMSMMAHRVKVIPYSTFR 469
>pdb|1SEZ|A Chain A, Crystal Structure Of Protoporphyrinogen Ix Oxidase
pdb|1SEZ|B Chain B, Crystal Structure Of Protoporphyrinogen Ix Oxidase
Length = 504
Score = 32.0 bits (71), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 13/41 (31%), Positives = 21/41 (51%)
Query: 729 RLQTAGISTIILEQRDKPGGRAYVYKQDGFIFDAGPTVITD 769
+L+ G++ + E K GG+ QDG I+D G T+
Sbjct: 31 KLKIHGLNVTVFEAEGKAGGKLRSVSQDGLIWDEGANTXTE 71
>pdb|3EUJ|B Chain B, Crystal Structure Of Muke-Mukf(Residues 292-443)-Mukb(Head
Domain)- Atpgammas Complex, Symmetric Dimer
pdb|3EUK|E Chain E, Crystal Structure Of Muke-Mukf(Residues 292-443)-Mukb(Head
Domain)- Atpgammas Complex, Asymmetric Dimer
pdb|3EUK|J Chain J, Crystal Structure Of Muke-Mukf(Residues 292-443)-Mukb(Head
Domain)- Atpgammas Complex, Asymmetric Dimer
Length = 152
Score = 32.0 bits (71), Expect = 2.6, Method: Composition-based stats.
Identities = 16/55 (29%), Positives = 28/55 (50%), Gaps = 1/55 (1%)
Query: 186 EREEIGSIPIALKNEKIIKFKKTICVGLRANLLH-ATTGYSLPIAIQLAENIAKY 239
E E +G +P+AL+ E + + I ++A L H T + + L E +A+Y
Sbjct: 45 EMEAVGELPMALEYESLTDVQTQIVTAIQAELAHFRNTAQPINLGAVLQEQLARY 99
Score = 32.0 bits (71), Expect = 2.6, Method: Composition-based stats.
Identities = 16/55 (29%), Positives = 28/55 (50%), Gaps = 1/55 (1%)
Query: 586 EREEIGSIPIALKNEKIIKFKKTICVGLRANLLH-ATTGYSLPIAIQLAENIAKY 639
E E +G +P+AL+ E + + I ++A L H T + + L E +A+Y
Sbjct: 45 EMEAVGELPMALEYESLTDVQTQIVTAIQAELAHFRNTAQPINLGAVLQEQLARY 99
>pdb|4AHP|A Chain A, Crystal Structure Of Wild Type N-acetylneuraminic Acid Lyase
From Staphylococcus Aureus
pdb|4AHP|B Chain B, Crystal Structure Of Wild Type N-acetylneuraminic Acid Lyase
From Staphylococcus Aureus
pdb|4AHP|C Chain C, Crystal Structure Of Wild Type N-acetylneuraminic Acid Lyase
From Staphylococcus Aureus
pdb|4AHP|D Chain D, Crystal Structure Of Wild Type N-acetylneuraminic Acid Lyase
From Staphylococcus Aureus
Length = 298
Score = 30.8 bits (68), Expect = 5.3, Method: Composition-based stats.
Identities = 32/120 (26%), Positives = 55/120 (45%), Gaps = 19/120 (15%)
Query: 1256 IGFKMKEPAFLALQKIISIHSFPVHLLFEHLDGFEMDVMERTYITLDETLGYCYHVAGTI 1315
+G K P F L++I +FP L+ L GF+ +++ T +D +G Y+V G
Sbjct: 167 VGVKYTAPNFFLLERIRK--AFPDKLI---LSGFDEMLVQATISGVDGAIGSTYNVNGR- 220
Query: 1316 GLIIAHLIGVKEKDTLNCARNLGI--AFQLTNISRDVIDDFYVGRCYLPL-DWLRNEGLN 1372
+ + + AR I A+QL + S D+I+ Y L + LR+ G++
Sbjct: 221 ----------RARKIFDLARQGQIQEAYQLQHDSNDIIETVLSMGIYPTLKEILRHRGID 270
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
0.325 0.140 0.427
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 39,276,459
Number of Sequences: 62578
Number of extensions: 1567477
Number of successful extensions: 4533
Number of sequences better than 100.0: 37
Number of HSP's better than 100.0 without gapping: 25
Number of HSP's successfully gapped in prelim test: 12
Number of HSP's that attempted gapping in prelim test: 4468
Number of HSP's gapped (non-prelim): 64
length of query: 1428
length of database: 14,973,337
effective HSP length: 111
effective length of query: 1317
effective length of database: 8,027,179
effective search space: 10571794743
effective search space used: 10571794743
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 58 (26.9 bits)