RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy14515
(586 letters)
>2pqp_A HD7A, histone deacetylase 7A; HDAC, structural genomics, structural
genomics consortium, SGC; HET: TSN; 1.80A {Homo sapiens}
PDB: 2pqo_A* 2nvr_A 3c0y_A 3c0z_A 3c10_A* 2vqm_A*
2vqj_A* 2vqw_G 2vqq_A* 2vqo_A* 2vqv_A*
Length = 421
Score = 273 bits (699), Expect = 4e-86
Identities = 88/337 (26%), Positives = 138/337 (40%), Gaps = 67/337 (19%)
Query: 7 IKDPCKELGLVQRCKFIQPREATQEEILKKHTIEQIELLATTEGSTDVDALEQLSSHYDA 66
I +E GL +C+ ++ R+A+ EE+ H+ + L T S +L+
Sbjct: 69 IWSRLQERGLRSQCECLRGRKASLEELQSVHSERHVLLYGTNPLSRLKLDNGKLAGLLAQ 128
Query: 67 IYIHPSSYKLSLLSAGSTIELRRNQKRNGSHSSSYKLSLLSAGSTIELVDNICRGEIKNG 126
+ + + S + +AGS +L + E+KNG
Sbjct: 129 RMFVMLPCGGVGVDTDTIW----------NELHSSNAARWAAGSVTDLAFKVASRELKNG 178
Query: 127 MAVIRPPGHHAMKSEYCGYCFFNNVALAAQHALDNTSVSRVLIVDWDVHHGQATQQMFYN 186
AV+RPPGHHA S G+CFFN+VA+A + + S++LIVDWDVHHG TQQ FY
Sbjct: 179 FAVVRPPGHHADHSTAMGFCFFNSVAIACRQLQQQSKASKILIVDWDVHHGNGTQQTFYQ 238
Query: 187 DNRVVYFSIHRYEHGTFWPNLRESEYDHIGEGIGKGYNFNIPLN---KTHMKDADYMAVF 243
D V+Y S+HR++ G F+P D +G G G+G+N N+ M D +Y+A F
Sbjct: 239 DPSVLYISLHRHDDGNFFPG--SGAVDEVGAGSGEGFNVNVAWAGGLDPPMGDPEYLAAF 296
Query: 244 HQVLLPMVAE-------------------------------------------------- 253
V++P+ E
Sbjct: 297 RIVVMPIAREFSPDLVLVSAGFDAAEGHPAPLGGYHVSAKCFGYMTQQLMNLAGGAVVLA 356
Query: 254 --GGYCLKSLAEGAALTLRALLDDPCPNFETLGTPSE 288
GG+ L ++ + + + ALL + G +
Sbjct: 357 LEGGHDLTAICDASEACVAALLGNRVDPLSEEGWKQK 393
Score = 155 bits (394), Expect = 4e-42
Identities = 54/124 (43%), Positives = 78/124 (62%), Gaps = 5/124 (4%)
Query: 358 KGMSDPEYIAAFQQVILPIAYQFNPELVLVSAGYDACVND--PLGGCKVSPEAYAHFTHW 415
M DPEY+AAF+ V++PIA +F+P+LVLVSAG+DA PLGG VS + + + T
Sbjct: 285 PPMGDPEYLAAFRIVVMPIAREFSPDLVLVSAGFDAAEGHPAPLGGYHVSAKCFGYMTQQ 344
Query: 416 LKALAQGRIILALEGGYNISSISYAMTLCTKALLG---DPLPLLESDLDINSSAVTSIKV 472
L LA G ++LALEGG+++++I A C ALLG DPL N +A+ S++
Sbjct: 345 LMNLAGGAVVLALEGGHDLTAICDASEACVAALLGNRVDPLSEEGWKQKPNLNAIRSLEA 404
Query: 473 IIII 476
+I +
Sbjct: 405 VIRV 408
>1zz1_A Histone deacetylase-like amidohydrolase; HET: SHH; 1.57A
{Alcaligenaceae bacterium} PDB: 1zz0_A* 1zz3_A* 2gh6_A*
2vcg_A*
Length = 369
Score = 236 bits (604), Expect = 1e-72
Identities = 71/243 (29%), Positives = 104/243 (42%), Gaps = 39/243 (16%)
Query: 12 KELGLVQRCKFIQPREATQEEILKKHTIEQIELLATTEGSTDVDALEQLSSHYDAI-YIH 70
G ++ I AT +IL+ H+ +E + L D I +
Sbjct: 51 CASGQIEHLTPIAAVAATDADILRAHSAAHLENMKRVS------NLPTGGDTGDGITMMG 104
Query: 71 PSSYKLSLLSAGSTIELRRNQKRNGSHSSSYKLSLLSAGSTIELVDNICRGEIKNGMAVI 130
+ A LSAG +EL + GE+ G A++
Sbjct: 105 NGGLE----IA-----------------------RLSAGGAVELTRRVATGELSAGYALV 137
Query: 131 RPPGHHAMKSEYCGYCFFNNVALAAQHALDNTSVSRVLIVDWDVHHGQATQQMFYNDNRV 190
PPGHHA + G+C FNN ++AA +A + RV I+DWDVHHG TQ +++ND V
Sbjct: 138 NPPGHHAPHNAAMGFCIFNNTSVAAGYARAVLGMERVAILDWDVHHGNGTQDIWWNDPSV 197
Query: 191 VYFSIHRYEHGTFWPNLRESEYDHIGEGIGKGYNFNIPLNKTHMKDADYMAVFHQVLLPM 250
+ S+H+ H F P+ G G G GYN N+PL +A Y+ QV+LP
Sbjct: 198 LTISLHQ--HLCFPPD--SGYSTERGAGNGHGYNINVPLPP-GSGNAAYLHAMDQVVLPA 252
Query: 251 VAE 253
+
Sbjct: 253 LRA 255
Score = 149 bits (377), Expect = 4e-40
Identities = 30/109 (27%), Positives = 48/109 (44%), Gaps = 7/109 (6%)
Query: 357 SKGMSDPEYIAAFQQVILPIAYQFNPELVLVSAGYDACVNDPLGGCKVSPEAYAHFTHWL 416
G + Y+ A QV+LP + P+L++V +G+DA + DPL V+ + +
Sbjct: 233 PPGSGNAAYLHAMDQVVLPALRAYRPQLIIVGSGFDASMLDPLARMMVTADGFRQMARRT 292
Query: 417 KALA----QGRIILALEGGYNISSISYAMTLCTKALLGD---PLPLLES 458
A GRI+ EGGY+ + + + L G P P E
Sbjct: 293 IDCAADICDGRIVFVQEGGYSPHYLPFCGLAVIEELTGVRSLPDPYHEF 341
>3men_A Acetylpolyamine aminohydrolase; histone deacetylase; 2.20A
{Burkholderia pseudomallei 1710B}
Length = 362
Score = 212 bits (541), Expect = 1e-63
Identities = 69/319 (21%), Positives = 108/319 (33%), Gaps = 67/319 (21%)
Query: 7 IKDPCKELGLVQRCKFIQPREATQEEILKKHTIEQIELLATTEGSTDVDALEQLSSHYDA 66
+ +G +P + I H + L T +
Sbjct: 57 LVAAAFAMGFP----VREPDDFGIAPIAAVHDTHYLRFLETVHREWKAMPEDWGDEAMSN 112
Query: 67 IYIHPSSYKLSLLSAGSTIELRRNQKRNGS---HSSSYKLSLLSAGSTIELVDNICRGEI 123
I++ + +L+ + +GS +++ + SA S + + G
Sbjct: 113 IFVREPNALRGVLAQAARHLA------DGSCPVGEHTWRAAYWSAQSALAAAAAVRDGA- 165
Query: 124 KNGMAVIRPPGHHAMKSEYCGYCFFNNVALAAQHALDNTSVSRVLIVDWDVHHGQATQQM 183
A+ RPPGHHA G+C+ NN A+AAQ +RV ++D D+HHGQ Q++
Sbjct: 166 PAAYALCRPPGHHARVDAAGGFCYLNNAAIAAQALRAR--HARVAVLDTDMHHGQGIQEI 223
Query: 184 FYNDNRVVYFSIHRYEHGTFWPNLRESEYDHIGEGIGKGYNFNIPLNKTHMKDADYMAVF 243
FY V+Y SIH F+P + + D G G G GYN N+P+ +A +
Sbjct: 224 FYARRDVLYVSIHGD-PTNFYPAVAGFD-DERGAGEGLGYNVNLPMPH-GSSEAAFFERV 280
Query: 244 HQVL----------------------------------------------LPMVA--EGG 255
L LP V EGG
Sbjct: 281 DDALRELRRFAPDALVLSLGFDVYRDDPQSQVAVTTDGFGRLGHLIGALRLPTVIVQEGG 340
Query: 256 YCLKSLAEGAALTLRALLD 274
Y ++SL A
Sbjct: 341 YHIESLEANARSFFGGFGA 359
Score = 120 bits (303), Expect = 4e-30
Identities = 20/92 (21%), Positives = 37/92 (40%), Gaps = 2/92 (2%)
Query: 359 GMSDPEYIAAFQQVILPIAYQFNPELVLVSAGYDACVNDPLGGCKVSPEAYAHFTHWLKA 418
G S+ + L +F P+ +++S G+D +DP V+ + + H + A
Sbjct: 270 GSSEAAFFERVDDA-LRELRRFAPDALVLSLGFDVYRDDPQSQVAVTTDGFGRLGHLIGA 328
Query: 419 LAQGRIILALEGGYNISSISYAMTLCTKALLG 450
L ++ EGGY+I S+
Sbjct: 329 LR-LPTVIVQEGGYHIESLEANARSFFGGFGA 359
>3q9b_A Acetylpolyamine amidohydrolase; HDAC, polyamines, arginase fold,
deacetylase, hydrolase-HYDR inhibitor complex; HET: B3N;
2.25A {Mycoplana ramosa} PDB: 3q9f_A* 3q9c_A* 3q9e_A*
Length = 341
Score = 201 bits (513), Expect = 7e-60
Identities = 69/317 (21%), Positives = 104/317 (32%), Gaps = 62/317 (19%)
Query: 7 IKDPCKELGLVQRCKFIQPREATQEEILKKHTIEQIELLATTEGSTDVDALEQLSSHYDA 66
I KE G + P E +LK H + L T
Sbjct: 36 ILAAVKEAGFDDV---VAPARHGLETVLKVHDAGYLNFLETAWD----RWKAAGYKGEAI 88
Query: 67 IYIHPSSYKLSLLSAGSTIELRRNQKRNGSHSS--SYKLSLLSAGSTIELVDNICRGEIK 124
P + ++ + S +++ +L S S I+ D I G K
Sbjct: 89 ATSFPVRRTSPRIPTDIEGQIGYYCNAAETAISPGTWEAALSSMASAIDGADLIAAGH-K 147
Query: 125 NGMAVIRPPGHHAMKSEYCGYCFFNNVALAAQHALDNTSVSRVLIVDWDVHHGQATQQMF 184
++ RPPGHHA + GYCF NN A+AAQ LD ++ I+D D HHG TQ +F
Sbjct: 148 AAFSLCRPPGHHAGIDMFGGYCFINNAAVAAQRLLDKG-AKKIAILDVDFHHGNGTQDIF 206
Query: 185 YNDNRVVYFSIHRYEHGTFWPNLRESEYDHIGEGIGKGYNFNIPLNKTHMKDADYMAVFH 244
Y V + S+H F L + G+G G G N P+ + + +
Sbjct: 207 YERGDVFFASLHGDPAEAFPHFL--GYAEETGKGAGAGTTANYPMGR-GTPYSVWGEALT 263
Query: 245 QVL----------------------------------------------LPMVA--EGGY 256
L +P++ EGGY
Sbjct: 264 DSLKRIAAFGAEAIVVSLGVDTFEQDPISFFKLTSPDYITMGRTIAASGVPLLVVMEGGY 323
Query: 257 CLKSLAEGAALTLRALL 273
+ + A L+ +
Sbjct: 324 GVPEIGLNVANVLKGVA 340
Score = 114 bits (286), Expect = 5e-28
Identities = 22/92 (23%), Positives = 37/92 (40%), Gaps = 2/92 (2%)
Query: 359 GMSDPEYIAAFQQVILPIAYQFNPELVLVSAGYDACVNDPLGGCKVSPEAYAHFTHWLKA 418
G + A + IA F E ++VS G D DP+ K++ Y + A
Sbjct: 252 GTPYSVWGEALTDSLKRIA-AFGAEAIVVSLGVDTFEQDPISFFKLTSPDYITMGRTIAA 310
Query: 419 LAQGRIILALEGGYNISSISYAMTLCTKALLG 450
+++ +EGGY + I + K + G
Sbjct: 311 SG-VPLLVVMEGGYGVPEIGLNVANVLKGVAG 341
>3ew8_A HD8, histone deacetylase 8; hydrolase, HDAC, metalloenzyme,
arginase fold, HDAC8, histon deacetylase, hydroxamate
inhibitor, unliganded; HET: B3N; 1.80A {Homo sapiens}
PDB: 3f06_A* 3ezp_A* 3ezt_A* 3f0r_A* 3f07_A* 2v5w_A*
2v5x_A* 3ewf_A* 3mz4_A* 3mz6_A* 3mz7_A* 3rqd_A* 3mz3_A*
1t64_A* 1t67_A* 1t69_A* 1vkg_A* 1w22_A* 3sff_A* 3sfh_A*
Length = 388
Score = 197 bits (502), Expect = 1e-57
Identities = 52/247 (21%), Positives = 97/247 (39%), Gaps = 33/247 (13%)
Query: 7 IKDPCKELGLVQRCKFIQPREATQEEILKKHTIEQIELLATTEGSTDVDALEQLSSHYDA 66
+ + L ++ + ++P+ A+ EE+ HT ++ L D D + + Y
Sbjct: 41 VHSLIEAYALHKQMRIVKPKVASMEEMATFHTDAYLQHLQKVSQEGDDDHPDSI--EYGL 98
Query: 67 IYIHPSSYKLSLLSAGSTIELRRNQKRNGSHSSSYKLSLLSAGSTIELVDNICRGEIKNG 126
Y+ P++ + + G+TI + G K
Sbjct: 99 GYLCPAT------------------------EGIFDYAAAIGGATITAAQCLIDGMCKVA 134
Query: 127 MAVIRPPGHHAMKSEYCGYCFFNNVALAAQHALDNTSVSRVLIVDWDVHHGQATQQMFYN 186
+ HHA K E G+C+ N+ L R+L VD D+HHG + F
Sbjct: 135 IN-WSGGWHHAKKDEASGFCYLNDAVLGILRLRRK--FERILYVDLDLHHGDGVEDAFSF 191
Query: 187 DNRVVYFSIHRYEHGTFWPNLRESEYDHIGEGIGKGYNFNIPLNKTHMKDADYMAVFHQV 246
++V+ S+H++ G F+P + +G G G+ Y+ N+P+ ++D Y + V
Sbjct: 192 TSKVMTVSLHKFSPG-FFPG--TGDVSDVGLGKGRYYSVNVPIQD-GIQDEKYYQICESV 247
Query: 247 LLPMVAE 253
L +
Sbjct: 248 LKEVYQA 254
Score = 122 bits (307), Expect = 2e-30
Identities = 22/97 (22%), Positives = 42/97 (43%), Gaps = 1/97 (1%)
Query: 358 KGMSDPEYIAAFQQVILPIAYQFNPELVLVSAGYDACVNDPLGGCKVSPEAYAHFTHWLK 417
G+ D +Y + V+ + FNP+ V++ G D DP+ ++P ++
Sbjct: 233 DGIQDEKYYQICESVLKEVYQAFNPKAVVLQLGADTIAGDPMCSFNMTPVGIGKCLKYIL 292
Query: 418 ALAQGRIILALEGGYNISSISYAMTLCTKALLGDPLP 454
++ GGYN+++ + T T +LG L
Sbjct: 293 QWQ-LATLILGGGGYNLANTARCWTYLTGVILGKTLS 328
>3max_A HD2, histone deacetylase 2; class 2, HDAC, foot pocket, hydrolase;
HET: LLX NHE; 2.05A {Homo sapiens}
Length = 367
Score = 196 bits (500), Expect = 2e-57
Identities = 62/248 (25%), Positives = 104/248 (41%), Gaps = 35/248 (14%)
Query: 7 IKDPCKELGLVQRCKFIQPREATQEEILKKHTIEQIELLATTEGSTDVDALEQLSSHYDA 66
+ GL ++ + +P +AT EE+ K H+ E I+ L + + +Q+ ++
Sbjct: 32 THNLLLNYGLYRKMEIYRPHKATAEEMTKYHSDEYIKFLRSIRPDNMSEYSKQM-QRFNV 90
Query: 67 IYIHPSSYKLSLLSAGSTIELRRNQKRNGSHSSSYKLSLLSAGSTIELVDNICRGEIKNG 126
P ++ LS G ++ + R +
Sbjct: 91 GEDCPVF------------------------DGLFEFCQLSTGGSVAGAVKLNRQ--QTD 124
Query: 127 MAVIRPPG-HHAMKSEYCGYCFFNNVALAAQHALDNTSVSRVLIVDWDVHHGQATQQMFY 185
MAV G HHA KSE G+C+ N++ LA L RVL +D D+HHG ++ FY
Sbjct: 125 MAVNWAGGLHHAKKSEASGFCYVNDIVLAILELLKY--HQRVLYIDIDIHHGDGVEEAFY 182
Query: 186 NDNRVVYFSIHRYEHGTFWPNLRESEYDHIGEGIGKGYNFNIPLNKTHMKDADYMAVFHQ 245
+RV+ S H+Y G ++P + IG G GK Y N P+ + D Y +F
Sbjct: 183 TTDRVMTVSFHKY--GEYFPG--TGDLRDIGAGKGKYYAVNFPMRD-GIDDESYGQIFKP 237
Query: 246 VLLPMVAE 253
++ ++
Sbjct: 238 IISKVMEM 245
Score = 124 bits (314), Expect = 2e-31
Identities = 22/97 (22%), Positives = 42/97 (43%), Gaps = 1/97 (1%)
Query: 358 KGMSDPEYIAAFQQVILPIAYQFNPELVLVSAGYDACVNDPLGGCKVSPEAYAHFTHWLK 417
G+ D Y F+ +I + + P V++ G D+ D LG ++ + +A +K
Sbjct: 224 DGIDDESYGQIFKPIISKVMEMYQPSAVVLQCGADSLSGDRLGCFNLTVKGHAKCVEVVK 283
Query: 418 ALAQGRIILALEGGYNISSISYAMTLCTKALLGDPLP 454
+++ GGY I +++ T T L +P
Sbjct: 284 TFN-LPLLMLGGGGYTIRNVARCWTYETAVALDCEIP 319
>1c3p_A Protein (HDLP (histone deacetylase-like protein) ); alpha/beta
fold, lyase; 1.80A {Aquifex aeolicus} SCOP: c.42.1.2
PDB: 1c3r_A* 1c3s_A*
Length = 375
Score = 193 bits (493), Expect = 2e-56
Identities = 70/326 (21%), Positives = 113/326 (34%), Gaps = 89/326 (27%)
Query: 7 IKDPCKELGLVQRCKFIQPREATQEEILKKHTIEQIELL--ATTEGSTDVDALEQLSSHY 64
+ + L+ + I+ R AT+EE+L HT + I L A A E+ +
Sbjct: 31 LLRFKDAMNLIDEKELIKSRPATKEELLLFHTEDYINTLMEAERCQCVPKGAREKYNIGG 90
Query: 65 DAIYIHPSSYKLSLLSAGSTIELRRNQKRNGSHSSSYKLSLLSAGSTIELVDNICRGEIK 124
+ + + S L+ GST++ ++ +G +
Sbjct: 91 YENPVSYAMFTGSSLATGSTVQA---------------------------IEEFLKGNV- 122
Query: 125 NGMAVIRPPG--HHAMKSEYCGYCFFNNVALAAQHALDNTSVSRVLIVDWDVHHGQATQQ 182
P G HHA KS G+C+ NN A+ ++ R+L +D D HH Q+
Sbjct: 123 ----AFNPAGGMHHAFKSRANGFCYINNPAVGIEYLRKKG-FKRILYIDLDAHHCDGVQE 177
Query: 183 MFYNDNRVVYFSIHRYEHGTFWPNLRESEYDHIGEGIGKGYNFNIPLNKTHMKDADYMAV 242
FY+ ++V S+H+ +P + + IGEG GKGYN NIPL K + D +++
Sbjct: 178 AFYDTDQVFVLSLHQS-PEYAFPF-EKGFLEEIGEGKGKGYNLNIPLPK-GLNDNEFLFA 234
Query: 243 FHQVLLP-------------------------------------------------MVAE 253
+ L +
Sbjct: 235 LEKSLEIVKEVFEPEVYLLQLGTDPLLEDYLSKFNLSNVAFLKAFNIVREVFGEGVYLGG 294
Query: 254 GGYCLKSLAEGAALTLRALLDDPCPN 279
GGY +LA L L P
Sbjct: 295 GGYHPYALARAWTLIWCELSGREVPE 320
Score = 125 bits (316), Expect = 1e-31
Identities = 25/97 (25%), Positives = 48/97 (49%), Gaps = 1/97 (1%)
Query: 358 KGMSDPEYIAAFQQVILPIAYQFNPELVLVSAGYDACVNDPLGGCKVSPEAYAHFTHWLK 417
KG++D E++ A ++ + + F PE+ L+ G D + D L +S A+ + ++
Sbjct: 224 KGLNDNEFLFALEKSLEIVKEVFEPEVYLLQLGTDPLLEDYLSKFNLSNVAFLKAFNIVR 283
Query: 418 ALAQGRIILALEGGYNISSISYAMTLCTKALLGDPLP 454
+ G + GGY+ +++ A TL L G +P
Sbjct: 284 EVF-GEGVYLGGGGYHPYALARAWTLIWCELSGREVP 319
>4a69_A Histone deacetylase 3,; transcription, hydrolase; HET: I0P; 2.06A
{Homo sapiens}
Length = 376
Score = 180 bits (459), Expect = 1e-51
Identities = 51/250 (20%), Positives = 94/250 (37%), Gaps = 38/250 (15%)
Query: 7 IKDPCKELGLVQRCKFIQPREATQEEILKKHTIEQIELL--ATTEGSTDVDALEQLSSHY 64
GL ++ +P +A+Q ++ + H+ + I+ L + +
Sbjct: 32 THSLVLHYGLYKKMIVFKPYQASQHDMCRFHSEDYIDFLQRVSPTNMQGFTKSLNAFNVG 91
Query: 65 DAIYIHPSSYKLSLLSAGSTIELRRNQKRNGSHSSSYKLSLLSAGSTIELVDNICRGEIK 124
D + P ++ G++++ +
Sbjct: 92 DDCPVFPGLFEFCSRYTGASLQG---------------------------ATQLNNKICD 124
Query: 125 NGMAVIRPPG-HHAMKSEYCGYCFFNNVALAAQHALDNTSVSRVLIVDWDVHHGQATQQM 183
A+ G HHA K E G+C+ N++ + L RVL +D D+HHG Q+
Sbjct: 125 I--AINWAGGLHHAKKFEASGFCYVNDIVIGILELLKYHP--RVLYIDIDIHHGDGVQEA 180
Query: 184 FYNDNRVVYFSIHRYEHGTFWPNLRESEYDHIGEGIGKGYNFNIPLNKTHMKDADYMAVF 243
FY +RV+ S H+Y + F+P + +G G+ Y N+PL + D Y +F
Sbjct: 181 FYLTDRVMTVSFHKYGNY-FFPG--TGDMYEVGAESGRYYCLNVPLRD-GIDDQSYKHLF 236
Query: 244 HQVLLPMVAE 253
V+ +V
Sbjct: 237 QPVINQVVDF 246
Score = 124 bits (312), Expect = 3e-31
Identities = 21/97 (21%), Positives = 43/97 (44%), Gaps = 1/97 (1%)
Query: 358 KGMSDPEYIAAFQQVILPIAYQFNPELVLVSAGYDACVNDPLGGCKVSPEAYAHFTHWLK 417
G+ D Y FQ VI + + P +++ G D+ D LG +S + ++K
Sbjct: 225 DGIDDQSYKHLFQPVINQVVDFYQPTCIVLQCGADSLGCDRLGCFNLSIRGHGECVEYVK 284
Query: 418 ALAQGRIILALEGGYNISSISYAMTLCTKALLGDPLP 454
+ +++ GGY + +++ T T L+ + +
Sbjct: 285 SFN-IPLLVLGGGGYTVRNVARCWTYETSLLVEEAIS 320
>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 = 54.9 bits (131), Expect = 6e-08
Identities = 84/606 (13%), Positives = 163/606 (26%), Gaps = 142/606 (23%)
Query: 4 HVNIKDPCKELGLVQRCKFIQ--PREA-TQEE---ILK-KHTIEQIELLATT---EGSTD 53
V CK +Q P+ ++EE I+ K + L T +
Sbjct: 23 SVFEDAFVDNFD----CKDVQDMPKSILSKEEIDHIIMSKDAVSGTLRLFWTLLSKQEEM 78
Query: 54 VDAL--EQLSSHYDAIYIHPSSYKLSLLSAGSTIELRRNQKRNGSHSSSYKLSLLSAGST 111
V E L +Y + S I+ + Q + + L +
Sbjct: 79 VQKFVEEVLRINYKFLM--------------SPIKTEQRQPSMMTRMYIEQRDRLYNDNQ 124
Query: 112 IELVDNICRGE----IKNGMAVIRPPGH---HAM----KSEYCGYCFFNNVALAAQHALD 160
+ N+ R + ++ + +RP + + K+ +A
Sbjct: 125 VFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKT-----------WVALD-VCL 172
Query: 161 NTSVSRVLI--VDWDVHHGQAT--------QQMFYNDNRVVYFSIHRYEHGTFWPNLRES 210
+ V + + W ++ Q + S R +H + S
Sbjct: 173 SYKVQCKMDFKIFW-LNLKNCNSPETVLEMLQKLLYQIDPNWTS--RSDHSSNIKLRIHS 229
Query: 211 EYDHIGEGI-GKGYN-----------------FNIP---LNKTHMKD-ADYMAVFHQVLL 248
+ + K Y FN+ L T K D+++ +
Sbjct: 230 IQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHI 289
Query: 249 PMVAEGGYCLKSLAEGAALTLRAL-LDDPC---PNFETLGTP----------SERPKIWK 294
+ +L +L LD P P + W
Sbjct: 290 SLDHH----SMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWD 345
Query: 295 EGKQCLVLALKHIVPQNSILSNLDRASRRFKLLTFVHLPAENTDVPLLFLLQIPGCYPHR 354
K L I+ S L+ L+ A R P + +P + LL + +
Sbjct: 346 NWKHVNCDKLTTII--ESSLNVLEPAEYRKMFDRLSVFP-PSAHIPTI-LLSLIWFDVIK 401
Query: 355 TKSKGMSDPEYIAA-FQQVILPIAYQFNPELVLVSAGY-DACVNDPLGGCKVSPEAYAH- 411
SD + + L + Q + + + Y + K+ E H
Sbjct: 402 ------SDVMVVVNKLHKYSL-VEKQPKESTISIPSIYLELK-------VKLENEYALHR 447
Query: 412 --FTHW--LKALAQGRIILALEGGYNISSISYAMTLCTKALLGDPLPLLESDLD-----I 462
H+ K +I Y S I + + ++ D I
Sbjct: 448 SIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRMVFLDFRFLEQKI 507
Query: 463 NSSAVTSIKVIIIINNNNSVYLYCSHRTENPFAFLSFLSLKNITETILNCIYEHRPYWNC 522
+ I+N + Y + +N + + + IL+ + + C
Sbjct: 508 RHDSTAWNASGSILNTLQQLKFYKPYICDNDPKY------ERLVNAILDFLPKIEENLIC 561
Query: 523 YKFQDI 528
K+ D+
Sbjct: 562 SKYTDL 567
Score = 46.0 bits (108), Expect = 3e-05
Identities = 78/464 (16%), Positives = 139/464 (29%), Gaps = 112/464 (24%)
Query: 162 TSVSRVLIVDWDV-HHGQATQQMFYNDN-RVVY-FSIHRYEHGTFWPNLRESEYDHIGEG 218
+VS L + W + + Q F + R+ Y F + + P++ Y E
Sbjct: 59 DAVSGTLRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYI---EQ 115
Query: 219 IGKGYNFNIPLNKTHMKDADYMAVFHQVLLPMVAEGGYCLKSLAEGAALTLRALLDDPCP 278
+ YN N K ++ Q L L + + +L
Sbjct: 116 RDRLYNDNQVFAKYNVSRLQPYLKLRQ-----------ALLELRPAKNVLIDGVL----- 159
Query: 279 NFETLGTPSERPKIWKEGKQCLVLALKHIVPQNSILSNLDRASRRFKLLTF-VHLPAENT 337
G+ GK + L + + +D FK+ F ++L N+
Sbjct: 160 -----GS----------GKTWVALD---VCLSYKVQCKMD-----FKI--FWLNLKNCNS 194
Query: 338 DVPLLFLLQIPGCYPHRTKSKGMSDPEYIAAFQQVILPIAYQFNPELVLVSAGYDAC--- 394
+L +LQ ++ S ++ + + I I + +L S Y+ C
Sbjct: 195 PETVLEMLQK---LLYQIDPNWTSRSDHSSNIKLRIHSIQAELR--RLLKSKPYENCLLV 249
Query: 395 ---VNDP------LGGCKV---SPEAYAHFTHWLKALAQGRIILA-LEGGYNISSISYAM 441
V + CK+ + + T +L A I L +
Sbjct: 250 LLNVQNAKAWNAFNLSCKILLTT--RFKQVTDFLSAATTTHISLDHHSMTL---TPDEVK 304
Query: 442 TLCTKALLGDP--LPLLESDLDINSSAVTSIKVIIIINNNNSVYLYCSHRTENPFAFLSF 499
+L K L P LP L N ++ I I +N + ++
Sbjct: 305 SLLLKYLDCRPQDLP--REVLTTNPRRLSIIAESIRDGLA---------TWDN-WKHVNC 352
Query: 500 LSLKNITETILNCI--YEHRP-YWNCYKFQD---IST--------EGAHSSPLHIPRAEF 545
L I E+ LN + E+R + F I T + S + +
Sbjct: 353 DKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLH 412
Query: 546 KY---EGNPKQEIYATRDCYPIQSQEFVRLCDERLD---SLIAS 583
KY E PK+ + Y E + S++
Sbjct: 413 KYSLVEKQPKESTISIPSIY----LELKVKLENEYALHRSIVDH 452
Score = 29.4 bits (65), Expect = 4.1
Identities = 20/161 (12%), Positives = 45/161 (27%), Gaps = 46/161 (28%)
Query: 441 MTLCTKALLGDPLPLLESDLDINS------SAVTSIKVIIIINNNNSV-------YLYCS 487
K +L + D S ++ ++ II + ++V + S
Sbjct: 14 HQYQYKDILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTLRLFWTLLS 73
Query: 488 HRTENPFAFL--------SFLSLKNITETI------LNCIYEHRPYWNCYKFQDISTEGA 533
+ E F+ FL TE I + +N +
Sbjct: 74 KQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYN---------DNQ 124
Query: 534 HSSPLHIPRAEFKYEGNPKQEIYATRDC-YPIQSQEFVRLC 573
+ ++ R + P ++ R ++ + V +
Sbjct: 125 VFAKYNVSRLQ------PYLKL---RQALLELRPAKNVLID 156
Score = 29.1 bits (64), Expect = 5.7
Identities = 35/206 (16%), Positives = 66/206 (32%), Gaps = 69/206 (33%)
Query: 2 LKHVNIKDPCKELGLVQRCKFIQPREATQE---------EILKKH--TIEQIELLATTEG 50
LK+++ + ++L PRE E ++ T + + + +
Sbjct: 308 LKYLDCR--PQDL----------PREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKL 355
Query: 51 STDVDA-LEQLSS-----HYDAIYIHPSSYK-----LSLL-SAGSTIELRR--NQKRNGS 96
+T +++ L L +D + + P S LSL+ ++ N+ S
Sbjct: 356 TTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYS 415
Query: 97 ----HSSSYKLSL----LSAGSTIE--------LVD--NICRGEIKNGMAVIRPP----- 133
+S+ L +E +VD NI + + + PP
Sbjct: 416 LVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLI---PPYLDQY 472
Query: 134 -----GHHAMKSEYCG-YCFFNNVAL 153
GHH E+ F V L
Sbjct: 473 FYSHIGHHLKNIEHPERMTLFRMVFL 498
>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 = 52.4 bits (125), Expect = 4e-07
Identities = 96/599 (16%), Positives = 170/599 (28%), Gaps = 204/599 (34%)
Query: 17 VQRCKFIQ--PREATQEEILKKHTIEQIELLATTEG--STDVDALEQLSSHYDAIYIHPS 72
+ +F + P E T+ EL+ G S+ V+ + +D +
Sbjct: 32 QLQEQFNKILP-EPTEGFAADDEPTTPAELVGKFLGYVSSLVEPSKV--GQFDQVL---- 84
Query: 73 SYKLSLLSAGSTIELRRNQKRNGSHSSSYKLSLLSAGSTIELVDNICRGEIKN---GMAV 129
L L + L N H+ + KL L +T+ + IKN +
Sbjct: 85 --NLCLTEFENCY-LEGND----IHALAAKL-LQENDTTLVKTKEL----IKNYITARIM 132
Query: 130 IRPPGHHAMKSEYCGYCFFNNVALAAQHALDNTSVSRVLIVDWDVHHGQATQQMFYNDNR 189
+ P S AL + + + L+ + GQ N
Sbjct: 133 AKRPFDKKSNS-----------ALF-RAVGEGNAQ---LVA---IFGGQG--------NT 166
Query: 190 VVYFSIHRYEHGTFWPNLRESEYDHIGEGIGKGYNFNIPLNKTHMKDADYMAVFHQVLLP 249
YF E LR+ Y Y+ + D + + L
Sbjct: 167 DDYFE----E-------LRDL-YQT--------YHVLV---------GDLIKFSAETLSE 197
Query: 250 MVAEGGYCLKSLAEGAALTLRALLDDP---------------CP--------NF----ET 282
++ K +G L + L++P CP ++ +
Sbjct: 198 LIRTTLDAEKVFTQG--LNILEWLENPSNTPDKDYLLSIPISCPLIGVIQLAHYVVTAKL 255
Query: 283 LG-TPSE-RPKIWKEGKQCLVLALKHIVPQNSILSNLDRASRRFKLLTFVHLPAENTDVP 340
LG TP E R + + + +V +I S F +
Sbjct: 256 LGFTPGELRSYL-----KGATGHSQGLVTAVAIAETDSWES-------FF----VSVRKA 299
Query: 341 LLFLLQIPGC-----YPHRT---------KSKGMSDPEYIAA-----FQQVILPIAYQFN 381
+ L I G YP+ + P + + +QV + + N
Sbjct: 300 ITVLFFI-GVRCYEAYPNTSLPPSILEDSLENNEGVPSPMLSISNLTQEQVQDYVN-KTN 357
Query: 382 PELVLVSAGYDACVNDP----LGGCKVSPEAYAHFTHWL---KA---LAQGRIIL---AL 428
L + VN + G P++ L KA L Q RI L
Sbjct: 358 SHLPAGKQVEISLVNGAKNLVVSG---PPQSLYGLNLTLRKAKAPSGLDQSRIPFSERKL 414
Query: 429 EGGYN---IS----SISYAMTLCTKALLGDPLPLLESDLDINSSAVTSIKVIIIINNNNS 481
+ ++ S + + + D L+++++ N+ + I V
Sbjct: 415 KFSNRFLPVASPFHS-HL-LVPASDLINKD---LVKNNVSFNAKDI-QIPV--------- 459
Query: 482 VYLYCSHRTENPFAFLSFLSLKNITETILNCIYEHRPYWNCYKFQDISTEGAHSSPLHI 540
Y + + L LS +I+E I++CI W HI
Sbjct: 460 ---YDTFDGSD----LRVLS-GSISERIVDCIIRLPVKW---------ETTTQFKATHI 501
Score = 45.4 bits (107), Expect = 6e-05
Identities = 34/211 (16%), Positives = 62/211 (29%), Gaps = 62/211 (29%)
Query: 419 LAQGRIILALEGGYNISSISY--AMTL--CTKALLGDPLPLLESDLDINSSAVTSIKVII 474
L+ G +LE + + S+ A L +L +P +D + + A K
Sbjct: 11 LSHG----SLEHVLLVPTASFFIASQLQEQFNKILPEPTEGFAADDEPTTPAELVGK--- 63
Query: 475 IINNNNSVYL-YCSHRTE---------------NPF--AFL------SFL-SLKNITETI 509
+L Y S E F +L + L +T
Sbjct: 64 --------FLGYVSSLVEPSKVGQFDQVLNLCLTEFENCYLEGNDIHALAAKLLQENDTT 115
Query: 510 LNCIYEH-RPYWNCYKFQDISTEGAHSSPL--HIPRAEFK-Y-----EGNPK------QE 554
L E + Y + +S L + + +GN ++
Sbjct: 116 LVKTKELIKNYITARIMAKRPFDKKSNSALFRAVGEGNAQLVAIFGGQGNTDDYFEELRD 175
Query: 555 IYATRDCYPIQSQEFVRLCDERLDSLIASKS 585
+Y T Y + + ++ E L LI +
Sbjct: 176 LYQT---YHVLVGDLIKFSAETLSELIRTTL 203
Score = 37.3 bits (86), Expect = 0.015
Identities = 29/169 (17%), Positives = 51/169 (30%), Gaps = 60/169 (35%)
Query: 120 RGEIKNGMAVIRPPGHHAMKS--EYCGYCFFNNVALAAQHALDNTSVSRVLIVDWD---- 173
+G I GH S EY ALA+ ++ V+ ++
Sbjct: 1750 KGLIPADATFA---GH----SLGEYA--------ALAS--------LADVMSIE-SLVEV 1785
Query: 174 VHH-GQATQQMFYND--NRVVYFSIHRYEHGTFWPNLRESEYDHIGEGIGK--GY----- 223
V + G Q D R Y + G + + ++ E +GK G+
Sbjct: 1786 VFYRGMTMQVAVPRDELGRSNY-GMIAINPGRVAASFSQEALQYVVERVGKRTGWLVEIV 1844
Query: 224 NFNIP-------------------LNKTHMKDADYMAVFHQVLLPMVAE 253
N+N+ LN ++ D + + + L V
Sbjct: 1845 NYNVENQQYVAAGDLRALDTVTNVLNFIKLQKIDIIELQKSLSLEEVEG 1893
>3hl0_A Maleylacetate reductase; structur genomics, PSI-2, protein
structure initiative, midwest CENT structural genomics,
MCSG; HET: MSE NAD EPE; 1.60A {Agrobacterium tumefaciens
str}
Length = 353
Score = 29.5 bits (67), Expect = 2.8
Identities = 8/38 (21%), Positives = 12/38 (31%), Gaps = 6/38 (15%)
Query: 142 YCGYCFFNNVALAAQHALDNTSVSRVLIVDWDVHHGQA 179
CG V ++ H L L D+ H +
Sbjct: 227 LCGTVL-GAVGMSLHHKL-----CHTLGGSLDLPHAET 258
>3jzd_A Iron-containing alcohol dehydrogenase; YP_298327.1, putative
alcohol dehedrogenase, structural GENO joint center for
structural genomics; HET: MSE NAD PG4 P6G PGE; 2.10A
{Ralstonia eutropha}
Length = 358
Score = 29.5 bits (67), Expect = 2.8
Identities = 8/38 (21%), Positives = 13/38 (34%), Gaps = 6/38 (15%)
Query: 142 YCGYCFFNNVALAAQHALDNTSVSRVLIVDWDVHHGQA 179
CG V +A H L L +++ H +
Sbjct: 229 LCGTVL-GGVGMALHHKL-----CHTLGGSFNLPHAET 260
>3iv7_A Alcohol dehydrogenase IV; NP_602249.1, iron-containing alcohol
dehydrogenase, structur genomics, joint center for
structural genomics; HET: MSE; 2.07A {Corynebacterium
glutamicum}
Length = 364
Score = 28.4 bits (64), Expect = 7.7
Identities = 5/37 (13%), Positives = 10/37 (27%), Gaps = 6/37 (16%)
Query: 143 CGYCFFNNVALAAQHALDNTSVSRVLIVDWDVHHGQA 179
F + H + L +++ H Q
Sbjct: 229 AAVSF-ASAGSGLHHKI-----CHTLGGTFNLPHAQT 259
>3o4o_C Interleukin-1 receptor type 2; cytokine-receptor complex,
beta-trefoil, IG-like fold, immun; HET: NAG; 3.30A {Homo
sapiens}
Length = 339
Score = 27.7 bits (61), Expect = 9.9
Identities = 6/44 (13%), Positives = 10/44 (22%)
Query: 538 LHIPRAEFKYEGNPKQEIYATRDCYPIQSQEFVRLCDERLDSLI 581
L P +I +D + L L+
Sbjct: 140 LVCPDLSEFTRDKTDVKIQWYKDSLLLDKDNEKFLSVRGTTHLL 183
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
0.320 0.136 0.413
Gapped
Lambda K H
0.267 0.0705 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 8,987,448
Number of extensions: 544405
Number of successful extensions: 1037
Number of sequences better than 10.0: 1
Number of HSP's gapped: 985
Number of HSP's successfully gapped: 36
Length of query: 586
Length of database: 6,701,793
Length adjustment: 99
Effective length of query: 487
Effective length of database: 3,937,614
Effective search space: 1917618018
Effective search space used: 1917618018
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 (21.8 bits)
S2: 60 (26.9 bits)