RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 041063
(490 letters)
>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 = 613 bits (1582), Expect = 0.0
Identities = 157/395 (39%), Positives = 229/395 (57%), Gaps = 11/395 (2%)
Query: 44 MEEPTEGASLVSGPDGKKRRVSYFYEPTIGDYYYGQGHPMKPHRIRMAHNLIVHYGLHRR 103
MEEP E A G+ Y Y P P R M H+LI Y LH++
Sbjct: 1 MEEPEEPA-----DSGQSLVPVYIYSPEYVSM--CDSLAKIPKRASMVHSLIEAYALHKQ 53
Query: 104 MEVNRPFPAGPSDIRRFHTDEYVEFLASVSPESSGDPSFSRHLKRFNVGEDCPVFDGLFG 163
M + +P A ++ FHTD Y++ L VS E D S + +G CP +G+F
Sbjct: 54 MRIVKPKVASMEEMATFHTDAYLQHLQKVSQEGDDDHPDSIE---YGLGYLCPATEGIFD 110
Query: 164 FCQASAGGSIGAAVKLNRGDADIAVNWAGGLHHAKKSEASGFCYVNDIVLGILELLKVHR 223
+ A G +I AA L G +A+NW+GG HHAKK EASGFCY+ND VLGIL L +
Sbjct: 111 YAAAIGGATITAAQCLIDGMCKVAINWSGGWHHAKKDEASGFCYLNDAVLGILRLRRKFE 170
Query: 224 RVLYVDIDVHHGDGVEEAFYTTDRVMTVSFHKFGD-FFPGTGHIKDVGAGQGKFYALNVP 282
R+LYVD+D+HHGDGVE+AF T +VMTVS HKF FFPGTG + DVG G+G++Y++NVP
Sbjct: 171 RILYVDLDLHHGDGVEDAFSFTSKVMTVSLHKFSPGFFPGTGDVSDVGLGKGRYYSVNVP 230
Query: 283 LNDGLDDESFRGLFRPIIQKVMEVYQPDAVVLQCGADSLSGDRLGCFNLSVKGHADCLRF 342
+ DG+ DE + + ++++V + + P AVVLQ GAD+++GD + FN++ G CL++
Sbjct: 231 IQDGIQDEKYYQICESVLKEVYQAFNPKAVVLQLGADTIAGDPMCSFNMTPVGIGKCLKY 290
Query: 343 LRSFNVPLMVLGGGGYTIRNVARCWCYETAVAVGVEPDNKLPYNEYYEYFGPDYTLHVEP 402
+ + + ++LGGGGY + N ARCW Y T V +G +++P +E++ +GPDY L + P
Sbjct: 291 ILQWQLATLILGGGGYNLANTARCWTYLTGVILGKTLSSEIPDHEFFTAYGPDYVLEITP 350
Query: 403 CNMENLNAHKDMEKIRNTLLEQLSGLIHAPSVPFQ 437
+ N +++I N + L ++
Sbjct: 351 SCRPDRNEPHRIQQILNYIKGNLKHVVIEGRSHHH 385
>3max_A HD2, histone deacetylase 2; class 2, HDAC, foot pocket, hydrolase;
HET: LLX NHE; 2.05A {Homo sapiens}
Length = 367
Score = 605 bits (1561), Expect = 0.0
Identities = 249/368 (67%), Positives = 309/368 (83%), Gaps = 2/368 (0%)
Query: 61 KRRVSYFYEPTIGDYYYGQGHPMKPHRIRMAHNLIVHYGLHRRMEVNRPFPAGPSDIRRF 120
K++V Y+Y+ IG+YYYGQGHPMKPHRIRM HNL+++YGL+R+ME+ RP A ++ ++
Sbjct: 2 KKKVCYYYDGDIGNYYYGQGHPMKPHRIRMTHNLLLNYGLYRKMEIYRPHKATAEEMTKY 61
Query: 121 HTDEYVEFLASVSPESSGDPSFSRHLKRFNVGEDCPVFDGLFGFCQASAGGSIGAAVKLN 180
H+DEY++FL S+ P+ +S+ ++RFNVGEDCPVFDGLF FCQ S GGS+ AVKLN
Sbjct: 62 HSDEYIKFLRSIRPD--NMSEYSKQMQRFNVGEDCPVFDGLFEFCQLSTGGSVAGAVKLN 119
Query: 181 RGDADIAVNWAGGLHHAKKSEASGFCYVNDIVLGILELLKVHRRVLYVDIDVHHGDGVEE 240
R D+AVNWAGGLHHAKKSEASGFCYVNDIVL ILELLK H+RVLY+DID+HHGDGVEE
Sbjct: 120 RQQTDMAVNWAGGLHHAKKSEASGFCYVNDIVLAILELLKYHQRVLYIDIDIHHGDGVEE 179
Query: 241 AFYTTDRVMTVSFHKFGDFFPGTGHIKDVGAGQGKFYALNVPLNDGLDDESFRGLFRPII 300
AFYTTDRVMTVSFHK+G++FPGTG ++D+GAG+GK+YA+N P+ DG+DDES+ +F+PII
Sbjct: 180 AFYTTDRVMTVSFHKYGEYFPGTGDLRDIGAGKGKYYAVNFPMRDGIDDESYGQIFKPII 239
Query: 301 QKVMEVYQPDAVVLQCGADSLSGDRLGCFNLSVKGHADCLRFLRSFNVPLMVLGGGGYTI 360
KVME+YQP AVVLQCGADSLSGDRLGCFNL+VKGHA C+ +++FN+PL++LGGGGYTI
Sbjct: 240 SKVMEMYQPSAVVLQCGADSLSGDRLGCFNLTVKGHAKCVEVVKTFNLPLLMLGGGGYTI 299
Query: 361 RNVARCWCYETAVAVGVEPDNKLPYNEYYEYFGPDYTLHVEPCNMENLNAHKDMEKIRNT 420
RNVARCW YETAVA+ E N+LPYN+Y+EYFGPD+ LH+ P NM N N + MEKI+
Sbjct: 300 RNVARCWTYETAVALDCEIPNELPYNDYFEYFGPDFKLHISPSNMTNQNTPEYMEKIKQR 359
Query: 421 LLEQLSGL 428
L E L L
Sbjct: 360 LFENLRML 367
>4a69_A Histone deacetylase 3,; transcription, hydrolase; HET: I0P; 2.06A
{Homo sapiens}
Length = 376
Score = 592 bits (1527), Expect = 0.0
Identities = 221/376 (58%), Positives = 295/376 (78%), Gaps = 4/376 (1%)
Query: 61 KRRVSYFYEPTIGDYYYGQGHPMKPHRIRMAHNLIVHYGLHRRMEVNRPFPAGPSDIRRF 120
+ V+YFY+P +G+++YG GHPMKPHR+ + H+L++HYGL+++M V +P+ A D+ RF
Sbjct: 2 AKTVAYFYDPDVGNFHYGAGHPMKPHRLALTHSLVLHYGLYKKMIVFKPYQASQHDMCRF 61
Query: 121 HTDEYVEFLASVSPESSGDPSFSRHLKRFNVGEDCPVFDGLFGFCQASAGGSIGAAVKLN 180
H+++Y++FL VSP + F++ L FNVG+DCPVF GLF FC G S+ A +LN
Sbjct: 62 HSEDYIDFLQRVSPTNM--QGFTKSLNAFNVGDDCPVFPGLFEFCSRYTGASLQGATQLN 119
Query: 181 RGDADIAVNWAGGLHHAKKSEASGFCYVNDIVLGILELLKVHRRVLYVDIDVHHGDGVEE 240
DIA+NWAGGLHHAKK EASGFCYVNDIV+GILELLK H RVLY+DID+HHGDGV+E
Sbjct: 120 NKICDIAINWAGGLHHAKKFEASGFCYVNDIVIGILELLKYHPRVLYIDIDIHHGDGVQE 179
Query: 241 AFYTTDRVMTVSFHKFGD-FFPGTGHIKDVGAGQGKFYALNVPLNDGLDDESFRGLFRPI 299
AFY TDRVMTVSFHK+G+ FFPGTG + +VGA G++Y LNVPL DG+DD+S++ LF+P+
Sbjct: 180 AFYLTDRVMTVSFHKYGNYFFPGTGDMYEVGAESGRYYCLNVPLRDGIDDQSYKHLFQPV 239
Query: 300 IQKVMEVYQPDAVVLQCGADSLSGDRLGCFNLSVKGHADCLRFLRSFNVPLMVLGGGGYT 359
I +V++ YQP +VLQCGADSL DRLGCFNLS++GH +C+ +++SFN+PL+VLGGGGYT
Sbjct: 240 INQVVDFYQPTCIVLQCGADSLGCDRLGCFNLSIRGHGECVEYVKSFNIPLLVLGGGGYT 299
Query: 360 IRNVARCWCYETAVAVGVEPDNKLPYNEYYEYFGPDYTLHVE-PCNMENLNAHKDMEKIR 418
+RNVARCW YET++ V +LPY+EY+EYF PD+TLH + +EN N+ + +++IR
Sbjct: 300 VRNVARCWTYETSLLVEEAISEELPYSEYFEYFAPDFTLHPDVSTRIENQNSRQYLDQIR 359
Query: 419 NTLLEQLSGLIHAPSV 434
T+ E L L HAPSV
Sbjct: 360 QTIFENLKMLNHAPSV 375
>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 = 548 bits (1413), Expect = 0.0
Identities = 113/378 (29%), Positives = 177/378 (46%), Gaps = 13/378 (3%)
Query: 62 RRVSYFYEPTIGDYYYGQGHPMKPHRIRMAHNLIVHYGLHRRMEVNRPFPAGPSDIRRFH 121
++V G Y Y + HP+K R+ + L E+ + PA ++ FH
Sbjct: 2 KKVKLIGTLDYGKYRYPKNHPLKIPRVSLLLRFKDAMNLIDEKELIKSRPATKEELLLFH 61
Query: 122 TDEYVEFLASVSPESSGDPSFSRHLKRFNVG-EDCPVFDGLFGFCQASAGGSIGAAVKLN 180
T++Y+ L +++N+G + PV +F + G ++ A +
Sbjct: 62 TEDYINTLMEAERCQCVPK---GAREKYNIGGYENPVSYAMFTGSSLATGSTVQAIEEFL 118
Query: 181 RGDADIAVNWAGGLHHAKKSEASGFCYVNDIVLGILELLKV-HRRVLYVDIDVHHGDGVE 239
+G+ +A N AGG+HHA KS A+GFCY+N+ +GI L K +R+LY+D+D HH DGV+
Sbjct: 119 KGN--VAFNPAGGMHHAFKSRANGFCYINNPAVGIEYLRKKGFKRILYIDLDAHHCDGVQ 176
Query: 240 EAFYTTDRVMTVSFHKFGD--FFPGTGHIKDVGAGQGKFYALNVPLNDGLDDESFRGLFR 297
EAFY TD+V +S H+ + F G ++++G G+GK Y LN+PL GL+D F
Sbjct: 177 EAFYDTDQVFVLSLHQSPEYAFPFEKGFLEEIGEGKGKGYNLNIPLPKGLNDNEFLFALE 236
Query: 298 PIIQKVMEVYQPDAVVLQCGADSLSGDRLGCFNLSVKGHADCLRFLRSFNVPLMVLGGGG 357
++ V EV++P+ +LQ G D L D L FNLS +R + LGGGG
Sbjct: 237 KSLEIVKEVFEPEVYLLQLGTDPLLEDYLSKFNLSNVAFLKAFNIVREVFGEGVYLGGGG 296
Query: 358 YTIRNVARCWCYETAVAVGVEPDNKLPYNEYYEYFGPDYTLHVE----PCNMENLNAHKD 413
Y +AR W G E KL D+ + +E L
Sbjct: 297 YHPYALARAWTLIWCELSGREVPEKLNNKAKELLKSIDFEEFDDEVDRSYMLETLKDPWR 356
Query: 414 MEKIRNTLLEQLSGLIHA 431
++R + + L +
Sbjct: 357 GGEVRKEVKDTLEKAKAS 374
>1zz1_A Histone deacetylase-like amidohydrolase; HET: SHH; 1.57A
{Alcaligenaceae bacterium} PDB: 1zz0_A* 1zz3_A* 2gh6_A*
2vcg_A*
Length = 369
Score = 183 bits (467), Expect = 1e-53
Identities = 78/341 (22%), Positives = 132/341 (38%), Gaps = 22/341 (6%)
Query: 65 SYFYEPTIGDYYYGQGHPMKPHRIRMAHNLIVHYGLHRRMEVNRPFPAGPSDIRRFHTDE 124
S H P R H L+ G + A +DI R H+
Sbjct: 20 SLAAANLTARMQPISHHLAHPDTKRRFHELVCASGQIEHLTPIAAVAATDADILRAHSAA 79
Query: 125 YVEFLASVSPESSGDPSFSRHLKRFNVGEDCPVFDGLFGFCQASAGGSIGAAVKLNRGDA 184
++E + VS +G + +G + SAGG++ ++ G+
Sbjct: 80 HLENMKRVSNLPTG---------GDTGDGITMMGNGGLEIARLSAGGAVELTRRVATGEL 130
Query: 185 DIA---VNWAGGLHHAKKSEASGFCYVNDIVLGILELLKVH--RRVLYVDIDVHHGDGVE 239
VN G HHA + A GFC N+ + V RV +D DVHHG+G +
Sbjct: 131 SAGYALVNPPG--HHAPHNAAMGFCIFNNTSVAAGYARAVLGMERVAILDWDVHHGNGTQ 188
Query: 240 EAFYTTDRVMTVSFHKFGDFFPGTGHIKDVGAGQGKFYALNVPLNDGLDDESFRGLFRPI 299
+ ++ V+T+S H+ F P +G+ + GAG G Y +NVPL G + ++ +
Sbjct: 189 DIWWNDPSVLTISLHQHLCFPPDSGYSTERGAGNGHGYNINVPLPPGSGNAAYLHAMDQV 248
Query: 300 IQKVMEVYQPDAVVLQCGADSLSGDRLGCFNLSVKGHADCLRFLRSF-----NVPLMVLG 354
+ + Y+P +++ G D+ D L ++ G R + ++ +
Sbjct: 249 VLPALRAYRPQLIIVGSGFDASMLDPLARMMVTADGFRQMARRTIDCAADICDGRIVFVQ 308
Query: 355 GGGYTIRNVARCWCYETAVAVGVEPDNKLPYNEYYEYFGPD 395
GGY+ + C GV PY+E+ G +
Sbjct: 309 EGGYSPHYLPFCGLAVIEELTGVRSL-PDPYHEFLAGMGGN 348
>3men_A Acetylpolyamine aminohydrolase; histone deacetylase; 2.20A
{Burkholderia pseudomallei 1710B}
Length = 362
Score = 175 bits (446), Expect = 1e-50
Identities = 77/312 (24%), Positives = 120/312 (38%), Gaps = 31/312 (9%)
Query: 79 QGHPMKPHRIRMAHNLIVHYGLHRRMEVNRPFPAGPSDIRRFHTDEYVEFLASVSPESSG 138
+ P R G R P G + I H Y+ FL +V E
Sbjct: 45 RMPQEVPERAARLVAAAFAMGFPVR----EPDDFGIAPIAAVHDTHYLRFLETVHREWKA 100
Query: 139 DP--------------------SFSRHLKRFNVGEDCPVFDGLFGFCQASAGGSIGAAVK 178
P R CPV + + SA ++ AA
Sbjct: 101 MPEDWGDEAMSNIFVREPNALRGVLAQAARHLADGSCPVGEHTWRAAYWSAQSALAAAAA 160
Query: 179 LNRGD--ADIAVNWAGGLHHAKKSEASGFCYVNDIVLGILELLKVHRRVLYVDIDVHHGD 236
+ G A G HHA+ A GFCY+N+ + L H RV +D D+HHG
Sbjct: 161 VRDGAPAAYALCRPPG--HHARVDAAGGFCYLNNAAIAAQALRARHARVAVLDTDMHHGQ 218
Query: 237 GVEEAFYTTDRVMTVSFHKF-GDFFPG-TGHIKDVGAGQGKFYALNVPLNDGLDDESFRG 294
G++E FY V+ VS H +F+P G + GAG+G Y +N+P+ G + +F
Sbjct: 219 GIQEIFYARRDVLYVSIHGDPTNFYPAVAGFDDERGAGEGLGYNVNLPMPHGSSEAAFFE 278
Query: 295 LFRPIIQKVMEVYQPDAVVLQCGADSLSGDRLGCFNLSVKGHADCLRFLRSFNVPLMVLG 354
++++ + PDA+VL G D D ++ G + + +P +++
Sbjct: 279 RVDDALRELRR-FAPDALVLSLGFDVYRDDPQSQVAVTTDGFGRLGHLIGALRLPTVIVQ 337
Query: 355 GGGYTIRNVARC 366
GGY I ++
Sbjct: 338 EGGYHIESLEAN 349
>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 = 172 bits (438), Expect = 5e-49
Identities = 84/371 (22%), Positives = 145/371 (39%), Gaps = 37/371 (9%)
Query: 45 EEPTEGASLVSGPDGKKRRVS----YFYEPTIG----DYYYGQGHPMKPHRIRMAHNLIV 96
EP A ++S + R + Y+ + HP RI+ + +
Sbjct: 15 PEPASQARVLSSSETPARTLPFTTGLIYDSVMLKHQCSCGDNSRHPEHAGRIQSIWSRLQ 74
Query: 97 HYGLHRRMEVNRPFPAGPSDIRRFHTDEYVEFLASVSPESSGDPSFSRHLKRFNVGEDCP 156
GL + E R A +++ H++ +V + +
Sbjct: 75 ERGLRSQCECLRGRKASLEELQSVHSERHVLLYGTNPLSRLKLDNGKLAGLLAQRMFVML 134
Query: 157 VFDGLFG------FCQAS-------AGGSIGAAVKLNRGDADIA---VNWAGGLHHAKKS 200
G+ S AG A K+ + V G HHA S
Sbjct: 135 PCGGVGVDTDTIWNELHSSNAARWAAGSVTDLAFKVASRELKNGFAVVRPPG--HHADHS 192
Query: 201 EASGFCYVNDIVLGILELLKVH--RRVLYVDIDVHHGDGVEEAFYTTDRVMTVSFHKF-- 256
A GFC+ N + + +L + ++L VD DVHHG+G ++ FY V+ +S H+
Sbjct: 193 TAMGFCFFNSVAIACRQLQQQSKASKILIVDWDVHHGNGTQQTFYQDPSVLYISLHRHDD 252
Query: 257 GDFFPGTGHIKDVGAGQGKFYALNVPLNDGLD----DESFRGLFRPIIQKVMEVYQPDAV 312
G+FFPG+G + +VGAG G+ + +NV GLD D + FR ++ + + PD V
Sbjct: 253 GNFFPGSGAVDEVGAGSGEGFNVNVAWAGGLDPPMGDPEYLAAFRIVVMPIAREFSPDLV 312
Query: 313 VLQCGADSLSGDR--LGCFNLSVKGHADCLRFLRSF-NVPLMVLGGGGYTIRNVARCWCY 369
++ G D+ G LG +++S K + L + +++ GG+ + +
Sbjct: 313 LVSAGFDAAEGHPAPLGGYHVSAKCFGYMTQQLMNLAGGAVVLALEGGHDLTAICDASEA 372
Query: 370 ETAVAVGVEPD 380
A +G D
Sbjct: 373 CVAALLGNRVD 383
>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 = 166 bits (422), Expect = 2e-47
Identities = 57/315 (18%), Positives = 107/315 (33%), Gaps = 32/315 (10%)
Query: 78 GQGHPMKPHRIRMAHNLIVHYGLHRRMEVNRPFPAGPSDIRRFHTDEYVEFLASVSPESS 137
P R + G + P G + + H Y+ FL +
Sbjct: 23 LVPPFEAPFRAEWILAAVKEAGFDDVVA---PARHGLETVLKVHDAGYLNFLETAWDRWK 79
Query: 138 GDP---------------------SFSRHLKRFNVGEDCPVFDGLFGFCQASAGGSIGAA 176
+ + + + G + +S +I A
Sbjct: 80 AAGYKGEAIATSFPVRRTSPRIPTDIEGQIGYYCNAAETAISPGTWEAALSSMASAIDGA 139
Query: 177 VKLNRGDADI--AVNWAGGLHHAKKSEASGFCYVNDIVLGILELLKVH-RRVLYVDIDVH 233
+ G G HHA G+C++N+ + LL +++ +D+D H
Sbjct: 140 DLIAAGHKAAFSLCRPPG--HHAGIDMFGGYCFINNAAVAAQRLLDKGAKKIAILDVDFH 197
Query: 234 HGDGVEEAFYTTDRVMTVSFHKF--GDFFPGTGHIKDVGAGQGKFYALNVPLNDGLDDES 291
HG+G ++ FY V S H F G+ ++ G G G N P+ G
Sbjct: 198 HGNGTQDIFYERGDVFFASLHGDPAEAFPHFLGYAEETGKGAGAGTTANYPMGRGTPYSV 257
Query: 292 FRGLFRPIIQKVMEVYQPDAVVLQCGADSLSGDRLGCFNLSVKGHADCLRFLRSFNVPLM 351
+ ++++ + +A+V+ G D+ D + F L+ + R + + VPL+
Sbjct: 258 WGEALTDSLKRIAA-FGAEAIVVSLGVDTFEQDPISFFKLTSPDYITMGRTIAASGVPLL 316
Query: 352 VLGGGGYTIRNVARC 366
V+ GGY + +
Sbjct: 317 VVMEGGYGVPEIGLN 331
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis,
programmed cell death; HET: DTP; 6.90A {Drosophila
melanogaster} PDB: 3iz8_A*
Length = 1221
Score = 40.6 bits (94), Expect = 0.001
Identities = 35/223 (15%), Positives = 58/223 (26%), Gaps = 75/223 (33%)
Query: 52 SLVSGPDGKKRRVSYFYEPTIGDYYYGQGHPMKPHRIRMA--HNLIV-HYGLHRRMEVNR 108
SLV +K+ +K H IV HY + + + +
Sbjct: 415 SLV-----EKQPKESTI------SIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDD 463
Query: 109 PFPAGPSDIRRFHTDEYV-EFLASVSPESSGDPSFSRHLKRFNVGEDCPVFDGL---FGF 164
P + D+Y + HLK E +F + F F
Sbjct: 464 LIPP--------YLDQYFYSHIG-------------HHLKNIEHPERMTLFRMVFLDFRF 502
Query: 165 CQASAGGSIGAAVKLNRGDADIAVNWAGGL-----------HHAKKSEASGFCYVNDIVL 213
+ K+ A N +G + + ++ VN
Sbjct: 503 LEQ----------KIRH--DSTAWNASGSILNTLQQLKFYKPYICDNDPKYERLVNA--- 547
Query: 214 GILELLKVHRRVLYVD--IDV------HHGDGV-EEAFYTTDR 247
IL+ L L D+ + + EEA R
Sbjct: 548 -ILDFLPKIEENLICSKYTDLLRIALMAEDEAIFEEAHKQVQR 589
Score = 32.9 bits (74), Expect = 0.28
Identities = 43/335 (12%), Positives = 94/335 (28%), Gaps = 120/335 (35%)
Query: 195 HHAKKSEAS--GFCYVNDIVLGILELLKVHRRVLYVDIDVHHGDGVEEAFYTTDRVMTVS 252
HH E + Y DI+ + + D V++ +++
Sbjct: 4 HHHMDFETGEHQYQY-KDILSVFEDAFVD-------NFDCKD---VQDM---PKSILS-- 47
Query: 253 FHKFGDFFPGTGHIKDVGAGQGKFYALNVPLNDGLDDESFRGLFRPIIQK--------VM 304
I + + LF ++ K V
Sbjct: 48 ----------KEEIDHI-------------IMSKDAVSGTLRLFWTLLSKQEEMVQKFVE 84
Query: 305 EVYQPD------AVVLQCGADSLSG-------DRLGCFN---LSVKGHA----------D 338
EV + + + + S+ DRL +N + K +
Sbjct: 85 EVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRL--YNDNQVFAKYNVSRLQPYLKLRQ 142
Query: 339 CLRFLRSFNVPLMVLGGGGYTIRNVARCWCYETAVAVGV----EPDNKLPYNEYYEYFGP 394
L LR +++ G G +T VA+ V + K+ + ++
Sbjct: 143 ALLELRP-AKNVLIDGVLG----------SGKTWVALDVCLSYKVQCKMDFKIFW----- 186
Query: 395 DYTLHVEPCNMENLNAHKDMEKIRNTLLEQLSGLIHAPSVPFQTTPATTQVPEEPEEDME 454
L+++ CN +LE L L++ + + + + ++
Sbjct: 187 ---LNLKNCNSPET------------VLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQ 231
Query: 455 RRPKPRIWNGEDYES-----DHDEDDKPPHMANFD 484
+ R+ + YE+ + ++ K F+
Sbjct: 232 AELR-RLLKSKPYENCLLVLLNVQNAK--AWNAFN 263
>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 = 40.0 bits (93), Expect = 0.002
Identities = 71/539 (13%), Positives = 141/539 (26%), Gaps = 237/539 (43%)
Query: 79 QGHPMKPHRIRMAHNLIVHYGLHRRMEVNRPFPAGP----SDIRRFHTDEYVEFLASVSP 134
+ +P L + +G +E P S ++ +++ + L +
Sbjct: 2 DAYSTRP--------LTLSHG---SLEHVLLVPTASFFIASQLQ----EQFNKILPEPTE 46
Query: 135 ESSGD--PSFSRHL-KRFNVGEDCPVFDGLFGFC----QASAGGSIGAAVKLNRGDADIA 187
+ D P+ L +F G+ + S G + L
Sbjct: 47 GFAADDEPTTPAELVGKF------------LGYVSSLVEPSKVGQFDQVLNL-------- 86
Query: 188 VNWAGGLHHAKKSEASGFCYVNDIVLGILELLKVHRRVLYVDIDVHHGDG----VEEAFY 243
L + + + NDI H + + + + +
Sbjct: 87 -----CLTEFE----NCYLEGNDI----------HALAAKLLQENDTTLVKTKELIKNYI 127
Query: 244 TTDRVMTVSFHKFGD--FFPGTGHIKDVGAGQGKFYAL-----NVPLNDGLDD-----ES 291
T + F K + F + VG G + A+ N +D ++ ++
Sbjct: 128 TARIMAKRPFDKKSNSALF------RAVGEGNAQLVAIFGGQGNT--DDYFEELRDLYQT 179
Query: 292 FRGLFRPIIQKVMEVYQPDAVVLQCGADSLSGDRLGCFNLSVKGHADCLRFLR------- 344
+ L +I+ A L L L + +G + L +L
Sbjct: 180 YHVLVGDLIKFS-------AETLS----ELIRTTLDAEKVFTQG-LNILEWLENPSNTPD 227
Query: 345 ---------SFNVPLMVLG----------GGGYTIRNVARCW-----CYE---TAVAVGV 377
S PL+ + G+T + + TAVA+
Sbjct: 228 KDYLLSIPISC--PLIGVIQLAHYVVTAKLLGFTPGELRSYLKGATGHSQGLVTAVAIAE 285
Query: 378 EPDNKLPYNEYYE----------YFG-------PDYTL----------HVE--PCNM--- 405
+ ++ + G P+ +L + E P M
Sbjct: 286 TDS----WESFFVSVRKAITVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGVPSPMLSI 341
Query: 406 ------------ENLNAHKDMEK---I------RNTLL----EQLSGL------IHAP-- 432
N+H K I +N ++ + L GL AP
Sbjct: 342 SNLTQEQVQDYVNKTNSHLPAGKQVEISLVNGAKNLVVSGPPQSLYGLNLTLRKAKAPSG 401
Query: 433 ----------------------SVPFQT---TPATTQVPEEPEEDMERRPKPRIWNGED 466
+ PF + PA+ + +D+ + +N +D
Sbjct: 402 LDQSRIPFSERKLKFSNRFLPVASPFHSHLLVPASDLI----NKDLVKNNVS--FNAKD 454
Score = 35.8 bits (82), Expect = 0.034
Identities = 43/292 (14%), Positives = 77/292 (26%), Gaps = 125/292 (42%)
Query: 32 KRHKREKSQLSKME----EPTEGASLVSGPDGKKRRVSYFYEPTIGDYYYGQGHPMKPHR 87
H ++ S ++ P G GK+ R +Y
Sbjct: 1650 DNHFKDTYGFSILDIVINNPVNLTIHFGGEKGKRIRENY--------------------- 1688
Query: 88 IRMAHNLIVHYGLHRRMEVNRPFPAGPSDIRR--FHTDEYV----EF------LASVSPE 135
A +I + +++ + F F +++ + +F L +
Sbjct: 1689 --SA--MIFETIVDGKLKTEKIFKEINEHSTSYTFRSEKGLLSATQFTQPALTLMEKAA- 1743
Query: 136 SSGDPSFSRHLK-RFNVGEDCPVFDG--------LFGFCQASAGG--SIGAAVKL--NRG 182
F LK + + D F G L AS SI + V++ RG
Sbjct: 1744 ------F-EDLKSKGLIPADA-TFAGHSLGEYAAL-----ASLADVMSIESLVEVVFYRG 1790
Query: 183 DAD----------------IAVN----WAGGLHHAKK------SEASG-FCY-VND---- 210
IA+N A A + + +G VN
Sbjct: 1791 MTMQVAVPRDELGRSNYGMIAINPGRVAASFSQEALQYVVERVGKRTGWLVEIVNYNVEN 1850
Query: 211 --IVLG-----------ILELLKVHRRVLYVDIDV------HHGDGVEEAFY 243
V +L +K+ + ID+ + VE +
Sbjct: 1851 QQYVAAGDLRALDTVTNVLNFIKLQK------IDIIELQKSLSLEEVEGHLF 1896
>2pff_A Fatty acid synthase subunit alpha, 3-oxoacyl-[acyl-carrier-PR; fatty
acid synthase, acyl-carrier-protein, beta-ketoacyl RED
beta-ketoacyl synthase, dehydratase; 4.00A {Saccharomyces
cerevisiae}
Length = 1688
Score = 38.3 bits (89), Expect = 0.007
Identities = 13/59 (22%), Positives = 19/59 (32%), Gaps = 21/59 (35%)
Query: 155 CPVFDGLFGFCQASAGGSIGAAVKLNR-GDADIAVNWAGGLHHAKKSEAS------GFC 206
PV G C A++ S+ V+ G A I + GG + F
Sbjct: 1101 TPV-----GAC-ATSVESVDIGVETILSGKARICI--VGG------YDDFQEEGSFEFG 1145
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna;
HET: CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 33.0 bits (74), Expect = 0.098
Identities = 8/23 (34%), Positives = 11/23 (47%), Gaps = 6/23 (26%)
Query: 37 EKSQLSKMEEPTEGASL-VSGPD 58
EK L K++ ASL + D
Sbjct: 18 EKQALKKLQ-----ASLKLYADD 35
Score = 29.1 bits (64), Expect = 1.9
Identities = 5/38 (13%), Positives = 17/38 (44%), Gaps = 15/38 (39%)
Query: 300 IQKV---MEVYQPDAVVLQCGADSLSGDRLGCFNLSVK 334
++K+ +++Y D+ A +L+ +++
Sbjct: 22 LKKLQASLKLYADDS------APALA------IKATME 47
>2bll_A Protein YFBG; decarboxylase, short chain dehydrogenase, L-ARA4N
biosynthes methyltransferase, transferase; 2.3A
{Escherichia coli} SCOP: c.2.1.2 PDB: 1u9j_A 1z73_A
1z75_A 1z7b_A 1z74_A
Length = 345
Score = 32.8 bits (75), Expect = 0.22
Identities = 23/118 (19%), Positives = 40/118 (33%), Gaps = 19/118 (16%)
Query: 347 NVPLMVLGGGGYTIRNVARCWCYETAVAVGVEPDNKLPYNEYYEYFGPDYTLHVEPCNME 406
P+ ++ GG RC+ + G+E ++ N G E N+
Sbjct: 207 GSPIKLIDGGKQK-----RCFTD---IRDGIEALYRIIENAGNRCDG-------EIINIG 251
Query: 407 NLNAHKDMEKIRNTLLEQL---SGLIHAPSVPFQTTPATTQVPEEPEEDMERRPKPRI 461
N +E++ LL H P ++ + +D+E R KP I
Sbjct: 252 NPENEASIEELGEMLLASFEKHPLRHHFPPFAGFRVVESSSYYGKGYQDVEHR-KPSI 308
>3ed6_A Betaine aldehyde dehydrogenase; structural genomics, infecti
deseases, NAD, oxidoreductase, PSI; 1.70A
{Staphylococcus aureus} PDB: 3fg0_A*
Length = 520
Score = 29.5 bits (67), Expect = 3.2
Identities = 10/27 (37%), Positives = 15/27 (55%), Gaps = 3/27 (11%)
Query: 49 EGASLVSG---PDGKKRRVSYFYEPTI 72
EGA++ G PD + F+EPT+
Sbjct: 374 EGATIAVGGKRPDRDDLKDGLFFEPTV 400
>3ty7_A Putative aldehyde dehydrogenase SAV2122; structural genomics,
PSI-biology, midwest center for structu genomics, MCSG;
HET: MSE; 2.40A {Staphylococcus aureus}
Length = 478
Score = 28.6 bits (65), Expect = 4.7
Identities = 12/28 (42%), Positives = 15/28 (53%), Gaps = 6/28 (21%)
Query: 49 EGASLVSG----PDGKKRRVSYFYEPTI 72
EGA L G P+G ++ YF PTI
Sbjct: 343 EGAELFYGGPGKPEGLEK--GYFARPTI 368
>3b4w_A Aldehyde dehydrogenase; RV0223C-NAD complex, structural genomics,
PSI-2, protein STR initiative; HET: NAD GOL; 1.80A
{Mycobacterium tuberculosis}
Length = 495
Score = 28.6 bits (65), Expect = 5.3
Identities = 11/27 (40%), Positives = 15/27 (55%), Gaps = 5/27 (18%)
Query: 49 EGASLVSG---PDGKKRRVSYFYEPTI 72
EGA LV G P+G +F +PT+
Sbjct: 349 EGARLVCGGGRPEGLDN--GFFIQPTV 373
>3ba0_A Macrophage metalloelastase; FULL-length MMP-12, hemopexin domain,
catalytic domain, domain interaction., calcium,
extracellular matrix; 3.00A {Homo sapiens} PDB: 2jxy_A
Length = 365
Score = 28.4 bits (62), Expect = 6.0
Identities = 28/121 (23%), Positives = 37/121 (30%), Gaps = 10/121 (8%)
Query: 177 VKLNRGDADIAVNWAGGLHHAKKSEASGFCYVNDIVLGILELLKVHRRVLYVDIDVHHGD 236
K+N G ADI V +A G H G + D GIL + D D
Sbjct: 45 SKINTGMADILVVFARGAH--------GDDHAFDGKGGILAHAFGPGSGIGGDAHF-DED 95
Query: 237 GVEEAFYTTDRVMTVSFHKFGDFFPGTGHIKDVGAGQGKFYALNVPLNDGLDDESFRGLF 296
+ + H+ G G GH D A Y L + RG+
Sbjct: 96 EFWTTHSGGTNLFLTAVHEIGHSL-GLGHSSDPKAVMFPTYKYVDINTFRLSADDIRGIQ 154
Query: 297 R 297
Sbjct: 155 S 155
>3u4j_A NAD-dependent aldehyde dehydrogenase; PSI-biology, nysgrc,
structural genomics, NEW YORK structura genomics
research consortium, tetramer; 2.00A {Sinorhizobium
meliloti}
Length = 528
Score = 28.3 bits (64), Expect = 6.1
Identities = 8/24 (33%), Positives = 12/24 (50%)
Query: 49 EGASLVSGPDGKKRRVSYFYEPTI 72
GA L+ G + R +Y PT+
Sbjct: 365 SGAELLLGGERIGREAGLYYAPTV 388
>3ayf_A Nitric oxide reductase; oxidoreductase; HET: HEM BOG EPE LOP; 2.50A
{Geobacillus stearothermophilus} PDB: 3ayg_A*
Length = 800
Score = 28.5 bits (63), Expect = 6.9
Identities = 11/29 (37%), Positives = 14/29 (48%), Gaps = 3/29 (10%)
Query: 391 YFGPDYT---LHVEPCNMENLNAHKDMEK 416
Y GPDYT L V M++ A + K
Sbjct: 93 YMGPDYTAEALKVYTEGMQDYKAKERYNK 121
>3pqa_A Lactaldehyde dehydrogenase; structural genomics, protein structure
initiative, nysgrc, P biology, oxidoreductase; 1.50A
{Methanocaldococcus jannaschii} PDB: 3rhd_A*
Length = 486
Score = 27.9 bits (63), Expect = 8.7
Identities = 10/24 (41%), Positives = 12/24 (50%), Gaps = 4/24 (16%)
Query: 49 EGASLVSGPDGKKRRVSYFYEPTI 72
EG L+ G GK R + PTI
Sbjct: 336 EGGKLLLG--GK--RDKALFYPTI 355
>3tx1_A UDP-N-acetylenolpyruvoylglucosamine reductase; structural genomics,
center for structural genomics of infec diseases, csgid;
HET: FAD; 2.69A {Listeria monocytogenes}
Length = 322
Score = 27.9 bits (63), Expect = 8.8
Identities = 5/20 (25%), Positives = 10/20 (50%)
Query: 337 ADCLRFLRSFNVPLMVLGGG 356
+ + + +PL +LG G
Sbjct: 68 QEVVAYCHQNKIPLTILGNG 87
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 0.140 0.437
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: 8,050,183
Number of extensions: 509247
Number of successful extensions: 1296
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1269
Number of HSP's successfully gapped: 43
Length of query: 490
Length of database: 6,701,793
Length adjustment: 97
Effective length of query: 393
Effective length of database: 3,993,456
Effective search space: 1569428208
Effective search space used: 1569428208
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: 59 (26.6 bits)