RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy8529
(436 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 = 114 bits (288), Expect = 2e-28
Identities = 76/362 (20%), Positives = 135/362 (37%), Gaps = 49/362 (13%)
Query: 97 EITSEPQESVVTRPWPIVYRPEYNVHFFKLEKLHPFDSKKWKHIFNYLWKHIFNYLVEAK 156
E EP +S + +Y PEY + K+ + + +
Sbjct: 2 EEPEEPADSGQSLVPVYIYSPEY----VSMCDSLAKIPKRASMVHSLI--------EAYA 49
Query: 157 FITQDNIIEPQEVSEEQLLIAHTEKYLKSLKWSFNVAAISEVCPLVAVPNYFVQKCYLRP 216
Q I++P+ S E++ HT+ YL+ L+ V+ + ++ C
Sbjct: 50 LHKQMRIVKPKVASMEEMATFHTDAYLQHLQ---KVSQEGDDDHPDSIEYGLGYLCPATE 106
Query: 217 MRYH-----VGGTLEAGFLALRRGWS---INIGGGFHHASETKGGGFCAYADISLLVK-L 267
+ G T+ A L G IN GG+HHA + + GFC D L + L
Sbjct: 107 GIFDYAAAIGGATITAA-QCLIDGMCKVAINWSGGWHHAKKDEASGFCYLNDAVLGILRL 165
Query: 268 LFQSKSISTAMIVDLDAHQGNGYEKDFMNETRIFIM---------------ETCITSKAK 312
+ + I + VDLD H G+G E F +++ + + +
Sbjct: 166 RRKFERI---LYVDLDLHHGDGVEDAFSFTSKVMTVSLHKFSPGFFPGTGDVSDVGLGKG 222
Query: 313 EAIRCRIELAPYTEDQHYLEKIEAGLERSLRSFCPDIIVYNAGTDVLLNDPLGLLAISPQ 372
+ + +D+ Y + E+ L+ ++F P +V G D + DP+ ++P
Sbjct: 223 RYYSVNVPIQDGIQDEKYYQICESVLKEVYQAFNPKAVVLQLGADTIAGDPMCSFNMTPV 282
Query: 373 GIIRRDELVFMKARERRVPIVMLTSGGY-LKQTARIIADSILNLADLGLISR-PYNIWFI 430
GI + + ++ ++L GGY L TAR + L S P + +F
Sbjct: 283 GIGK----CLKYILQWQLATLILGGGGYNLANTARCWTYLTGVILGKTLSSEIPDHEFFT 338
Query: 431 YY 432
Y
Sbjct: 339 AY 340
Score = 51.2 bits (123), Expect = 3e-07
Identities = 27/96 (28%), Positives = 37/96 (38%), Gaps = 29/96 (30%)
Query: 4 GTLEAGFLALRRGWS---INIGGGFHHASETKGGGFCAYADISLLVK-LLFQSKSISTAM 59
T+ A L G IN GG+HHA + + GFC D L + L + + I +
Sbjct: 118 ATITAA-QCLIDGMCKVAINWSGGWHHAKKDEASGFCYLNDAVLGILRLRRKFERI---L 173
Query: 60 IVDLDA---------------------HQFSDYYFP 74
VDLD H+FS +FP
Sbjct: 174 YVDLDLHHGDGVEDAFSFTSKVMTVSLHKFSPGFFP 209
>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 = 112 bits (283), Expect = 6e-28
Identities = 65/317 (20%), Positives = 116/317 (36%), Gaps = 46/317 (14%)
Query: 148 IFNYLVEAKFITQDNIIEPQEVSEEQLLIAHTEKYLKSLKWSFNVAAISEVCPLVAVP-- 205
+ + I + +I+ + ++E+LL+ HTE Y + + E VP
Sbjct: 31 LLRFKDAMNLIDEKELIKSRPATKEELLLFHTEDY---------INTLMEAERCQCVPKG 81
Query: 206 -----------NYFVQKCYLRPMRYHVGGTLEAGFLALRRGWSINIGGGFHHASETKGGG 254
N + G T++A L+ + N GG HHA +++ G
Sbjct: 82 AREKYNIGGYENPVSYAMFTGSSLA-TGSTVQAIEEFLKGNVAFNPAGGMHHAFKSRANG 140
Query: 255 FCAYADISLLVKLLFQSKSISTAMIVDLDAHQGNGYEKDFMNETRIFIMET--------- 305
FC + ++ ++ L + K + +DLDAH +G ++ F + ++F++
Sbjct: 141 FCYINNPAVGIEYL-RKKGFKRILYIDLDAHHCDGVQEAFYDTDQVFVLSLHQSPEYAFP 199
Query: 306 CITSKAKEAIRCR-------IELAPYTEDQHYLEKIEAGLERSLRSFCPDIIVYNAGTDV 358
+E + I L D +L +E LE F P++ + GTD
Sbjct: 200 FEKGFLEEIGEGKGKGYNLNIPLPKGLNDNEFLFALEKSLEIVKEVFEPEVYLLQLGTDP 259
Query: 359 LLNDPLGLLAISPQGIIRRDELVFMKARERRVPIVMLTSGGY-LKQTARIIADSILNLAD 417
LL D L +S ++ F RE V L GGY AR L+
Sbjct: 260 LLEDYLSKFNLSNVAFLK----AFNIVREVFGEGVYLGGGGYHPYALARAWTLIWCELSG 315
Query: 418 LGLISR-PYNIWFIYYT 433
+ + + +
Sbjct: 316 REVPEKLNNKAKELLKS 332
Score = 54.3 bits (131), Expect = 3e-08
Identities = 19/63 (30%), Positives = 34/63 (53%), Gaps = 1/63 (1%)
Query: 4 GTLEAGFLALRRGWSINIGGGFHHASETKGGGFCAYADISLLVKLLFQSKSISTAMIVDL 63
T++A L+ + N GG HHA +++ GFC + ++ ++ L + K + +DL
Sbjct: 109 STVQAIEEFLKGNVAFNPAGGMHHAFKSRANGFCYINNPAVGIEYL-RKKGFKRILYIDL 167
Query: 64 DAH 66
DAH
Sbjct: 168 DAH 170
>3max_A HD2, histone deacetylase 2; class 2, HDAC, foot pocket, hydrolase;
HET: LLX NHE; 2.05A {Homo sapiens}
Length = 367
Score = 112 bits (283), Expect = 6e-28
Identities = 68/345 (19%), Positives = 132/345 (38%), Gaps = 45/345 (13%)
Query: 113 IVYRPEYNVHFFKLEKLHPFDSKKWKHIFNYLWKHIFNYLVEAKFITQDNIIEPQEVSEE 172
Y + +++ + HP + + N L + + I P + + E
Sbjct: 7 YYYDGDIGNYYY--GQGHPMKPHRIRMTHNLL--------LNYGLYRKMEIYRPHKATAE 56
Query: 173 QLLIAHTEKYLKSLKWSFNVAAISEVCP-----LVAVPNYFVQKCYLRPMRYHVGGTLEA 227
++ H+++Y+K L+ S +SE V + GG++
Sbjct: 57 EMTKYHSDEYIKFLR-SIRPDNMSEYSKQMQRFNVGEDCPVFDGLFEFCQLS-TGGSVAG 114
Query: 228 GFLALRRGWS---INIGGGFHHASETKGGGFCAYADISLLVK-LLFQSKSISTAMIVDLD 283
+ L R + +N GG HHA +++ GFC DI L + LL + + + +D+D
Sbjct: 115 A-VKLNRQQTDMAVNWAGGLHHAKKSEASGFCYVNDIVLAILELLKYHQRV---LYIDID 170
Query: 284 AHQGNGYEKDFMNETRIFIM--------------ETCITSKAKEAIRCRIELAPYTEDQH 329
H G+G E+ F R+ + I + + + +D+
Sbjct: 171 IHHGDGVEEAFYTTDRVMTVSFHKYGEYFPGTGDLRDIGAGKGKYYAVNFPMRDGIDDES 230
Query: 330 YLEKIEAGLERSLRSFCPDIIVYNAGTDVLLNDPLGLLAISPQGIIRRDELVFMKARERR 389
Y + + + + + + P +V G D L D LG ++ +G + +
Sbjct: 231 YGQIFKPIISKVMEMYQPSAVVLQCGADSLSGDRLGCFNLTVKGHAK----CVEVVKTFN 286
Query: 390 VPIVMLTSGGY-LKQTARIIADSILNLADLGLISR-PYNIWFIYY 432
+P++ML GGY ++ AR D + + PYN +F Y+
Sbjct: 287 LPLLMLGGGGYTIRNVARCWTYETAVALDCEIPNELPYNDYFEYF 331
Score = 50.4 bits (121), Expect = 5e-07
Identities = 20/67 (29%), Positives = 34/67 (50%), Gaps = 8/67 (11%)
Query: 4 GTLEAGFLALRRGWS---INIGGGFHHASETKGGGFCAYADISLLVK-LLFQSKSISTAM 59
G++ + L R + +N GG HHA +++ GFC DI L + LL + + +
Sbjct: 110 GSVAGA-VKLNRQQTDMAVNWAGGLHHAKKSEASGFCYVNDIVLAILELLKYHQRV---L 165
Query: 60 IVDLDAH 66
+D+D H
Sbjct: 166 YIDIDIH 172
>4a69_A Histone deacetylase 3,; transcription, hydrolase; HET: I0P; 2.06A
{Homo sapiens}
Length = 376
Score = 110 bits (276), Expect = 7e-27
Identities = 65/349 (18%), Positives = 127/349 (36%), Gaps = 52/349 (14%)
Query: 113 IVYRPEYNVHFFKLEKLHPFDSKKWKHIFNYLWKHIFNYLVEAKFITQDNIIEPQEVSEE 172
Y P+ + HP + + + + + + +P + S+
Sbjct: 7 YFYDPDVGNFHY--GAGHPMKPHRLALTHSLV--------LHYGLYKKMIVFKPYQASQH 56
Query: 173 QLLIAHTEKYLKSLKWSFNVAAISEVCPLVAVPNYFVQK-CYLRPMRYH-----VGGTLE 226
+ H+E Y+ L+ V+ + ++ + V C + P + G +L+
Sbjct: 57 DMCRFHSEDYIDFLQ---RVSPTNMQGFTKSLNAFNVGDDCPVFPGLFEFCSRYTGASLQ 113
Query: 227 AGFLALRRGWS---INIGGGFHHASETKGGGFCAYADISLLVKLLFQSKSISTAMIVDLD 283
L IN GG HHA + + GFC DI + + L K + +D+D
Sbjct: 114 GA-TQLNNKICDIAINWAGGLHHAKKFEASGFCYVNDIVIGILELL--KYHPRVLYIDID 170
Query: 284 AHQGNGYEKDFMNETRIFIM---------------ETCITSKAKEAIRCRIELAPYTEDQ 328
H G+G ++ F R+ + + +++ + L +DQ
Sbjct: 171 IHHGDGVQEAFYLTDRVMTVSFHKYGNYFFPGTGDMYEVGAESGRYYCLNVPLRDGIDDQ 230
Query: 329 HYLEKIEAGLERSLRSFCPDIIVYNAGTDVLLNDPLGLLAISPQG---IIRRDELVFMKA 385
Y + + + + + P IV G D L D LG +S +G +
Sbjct: 231 SYKHLFQPVINQVVDFYQPTCIVLQCGADSLGCDRLGCFNLSIRGHGECVEY-------V 283
Query: 386 RERRVPIVMLTSGGY-LKQTARIIADSILNLADLGLISR-PYNIWFIYY 432
+ +P+++L GGY ++ AR L + + PY+ +F Y+
Sbjct: 284 KSFNIPLLVLGGGGYTVRNVARCWTYETSLLVEEAISEELPYSEYFEYF 332
Score = 48.1 bits (115), Expect = 3e-06
Identities = 22/95 (23%), Positives = 35/95 (36%), Gaps = 27/95 (28%)
Query: 4 GTLEAGFLALRRGWS---INIGGGFHHASETKGGGFCAYADISLLVKLLFQSKSISTAMI 60
+L+ L IN GG HHA + + GFC DI + + L K +
Sbjct: 110 ASLQGA-TQLNNKICDIAINWAGGLHHAKKFEASGFCYVNDIVIGILELL--KYHPRVLY 166
Query: 61 VDLDA---------------------HQFSDYYFP 74
+D+D H++ +Y+FP
Sbjct: 167 IDIDIHHGDGVQEAFYLTDRVMTVSFHKYGNYFFP 201
>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 = 84.0 bits (208), Expect = 4e-18
Identities = 58/301 (19%), Positives = 104/301 (34%), Gaps = 57/301 (18%)
Query: 146 KHIFNYLVEAKFITQDNIIEPQEVSEEQLLIAHTEKYLKSLKWSFNVAAISEVCPLVAVP 205
+ I + EA F D+++ P E +L H YL L+ +++ +
Sbjct: 34 EWILAAVKEAGF---DDVVAPARHGLETVLKVHDAGYLNFLETAWDRWKAAGYKGEAIAT 90
Query: 206 NYFVQKCYLRPMRYHVG---------------GTLEAGFLALRRGWSIN----IGGGF-- 244
++ V++ R G GT EA ++ +I+ I G
Sbjct: 91 SFPVRRTSPRIPTDIEGQIGYYCNAAETAISPGTWEAALSSM--ASAIDGADLIAAGHKA 148
Query: 245 ---------HHASETKGGGFCAYADISLLVKLLFQSKSISTAMIVDLDAHQGNGYEKDFM 295
HHA GG+C + ++ + L K I+D+D H GNG + F
Sbjct: 149 AFSLCRPPGHHAGIDMFGGYCFINNAAVAAQRL-LDKGAKKIAILDVDFHHGNGTQDIFY 207
Query: 296 NETRIFIMET---------CITSKAKEAIRCRIE-------LAPYTEDQHYLEKIEAGLE 339
+F A+E + + T + E + L+
Sbjct: 208 ERGDVFFASLHGDPAEAFPHFLGYAEETGKGAGAGTTANYPMGRGTPYSVWGEALTDSLK 267
Query: 340 RSLRSFCPDIIVYNAGTDVLLNDPLGLLAISPQGIIRRDELVFMKARERRVPIVMLTSGG 399
R + +F + IV + G D DP+ ++ I + VP++++ GG
Sbjct: 268 R-IAAFGAEAIVVSLGVDTFEQDPISFFKLTSPDYITMGRTI----AASGVPLLVVMEGG 322
Query: 400 Y 400
Y
Sbjct: 323 Y 323
Score = 35.1 bits (81), Expect = 0.040
Identities = 12/41 (29%), Positives = 19/41 (46%), Gaps = 1/41 (2%)
Query: 26 HHASETKGGGFCAYADISLLVKLLFQSKSISTAMIVDLDAH 66
HHA GG+C + ++ + L K I+D+D H
Sbjct: 158 HHAGIDMFGGYCFINNAAVAAQRL-LDKGAKKIAILDVDFH 197
>1zz1_A Histone deacetylase-like amidohydrolase; HET: SHH; 1.57A
{Alcaligenaceae bacterium} PDB: 1zz0_A* 1zz3_A* 2gh6_A*
2vcg_A*
Length = 369
Score = 77.8 bits (192), Expect = 8e-16
Identities = 42/253 (16%), Positives = 82/253 (32%), Gaps = 41/253 (16%)
Query: 148 IFNYLVEAKFITQDNIIEPQEVSEEQLLIAHTEKYLKSLKWSFNVAAISEVCPLVAVPNY 207
+ + I I ++ +L AH+ +L+++K V L +
Sbjct: 46 FHELVCASGQIEHLTPIAAVAATDADILRAHSAAHLENMK---------RVSNLPTGGDT 96
Query: 208 FVQKCYLRPMRYH-----VGGTLEAGFLALRRGWSINIGGGF-------HHASETKGGGF 255
+ GG +E + G+ HHA GF
Sbjct: 97 GDGITMMGNGGLEIARLSAGGAVELTRRVATG----ELSAGYALVNPPGHHAPHNAAMGF 152
Query: 256 CAYADISLLVKLLFQSKSISTAMIVDLDAHQGNGYEKDFMNETRIF-------------- 301
C + + S+ + I+D D H GNG + + N+ +
Sbjct: 153 CIFNNTSVAAGYARAVLGMERVAILDWDVHHGNGTQDIWWNDPSVLTISLHQHLCFPPDS 212
Query: 302 -IMETCITSKAKEAIRCRIELAPYTEDQHYLEKIEAGLERSLRSFCPDIIVYNAGTDVLL 360
+ L P + + YL ++ + +LR++ P +I+ +G D +
Sbjct: 213 GYSTERGAGNGHGYN-INVPLPPGSGNAAYLHAMDQVVLPALRAYRPQLIIVGSGFDASM 271
Query: 361 NDPLGLLAISPQG 373
DPL + ++ G
Sbjct: 272 LDPLARMMVTADG 284
Score = 34.6 bits (80), Expect = 0.060
Identities = 11/41 (26%), Positives = 16/41 (39%)
Query: 26 HHASETKGGGFCAYADISLLVKLLFQSKSISTAMIVDLDAH 66
HHA GFC + + S+ + I+D D H
Sbjct: 142 HHAPHNAAMGFCIFNNTSVAAGYARAVLGMERVAILDWDVH 182
>3men_A Acetylpolyamine aminohydrolase; histone deacetylase; 2.20A
{Burkholderia pseudomallei 1710B}
Length = 362
Score = 76.3 bits (188), Expect = 2e-15
Identities = 50/299 (16%), Positives = 94/299 (31%), Gaps = 56/299 (18%)
Query: 146 KHIFNYLVEAKFITQDNIIEPQEVSEEQLLIAHTEKYLKSLK--WSFNVAAISEVCPLVA 203
+ F + EP + + H YL+ L+ A +
Sbjct: 55 ARLVAAAFAMGFP----VREPDDFGIAPIAAVHDTHYLRFLETVHREWKAMPEDWGDEAM 110
Query: 204 VPNYFVQKCYLRPMRYHVG------------GTLEAGFLA------LRRGWSINIGGGF- 244
+ + LR + T A + + +
Sbjct: 111 SNIFVREPNALRGVLAQAARHLADGSCPVGEHTWRAAYWSAQSALAAAAAVRDGAPAAYA 170
Query: 245 ------HHASETKGGGFCAYADISLLVK-LLFQSKSISTAMIVDLDAHQGNGYEKDFMNE 297
HHA GGFC + ++ + L + + ++D D H G G ++ F
Sbjct: 171 LCRPPGHHARVDAAGGFCYLNNAAIAAQALRARHARV---AVLDTDMHHGQGIQEIFYAR 227
Query: 298 TRIFIMET---------CITSKAKE-------AIRCRIELAPYTEDQHYLEKIEAGLERS 341
+ + + E + + + + + E+++ L
Sbjct: 228 RDVLYVSIHGDPTNFYPAVAGFDDERGAGEGLGYNVNLPMPHGSSEAAFFERVDDALRE- 286
Query: 342 LRSFCPDIIVYNAGTDVLLNDPLGLLAISPQGIIRRDELVFMKARERRVPIVMLTSGGY 400
LR F PD +V + G DV +DP +A++ G R L+ R+P V++ GGY
Sbjct: 287 LRRFAPDALVLSLGFDVYRDDPQSQVAVTTDGFGRLGHLI----GALRLPTVIVQEGGY 341
Score = 31.3 bits (71), Expect = 0.61
Identities = 11/42 (26%), Positives = 19/42 (45%), Gaps = 4/42 (9%)
Query: 26 HHASETKGGGFCAYADISLLVK-LLFQSKSISTAMIVDLDAH 66
HHA GGFC + ++ + L + + ++D D H
Sbjct: 177 HHARVDAAGGFCYLNNAAIAAQALRARHARV---AVLDTDMH 215
>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 = 69.8 bits (171), Expect = 4e-13
Identities = 50/275 (18%), Positives = 91/275 (33%), Gaps = 51/275 (18%)
Query: 146 KHIFNYLVEAKFITQDNIIEPQEVSEEQLLIAHTEKYLKSLKWSFNVAAISEVCPLVAVP 205
+ I++ L E +Q + ++ S E+L H+E+++ + + L +
Sbjct: 67 QSIWSRLQERGLRSQCECLRGRKASLEELQSVHSERHVLLYGTNPLSRLKLDNGKLAGLL 126
Query: 206 NYFVQKC-------------YLRPMRYH-----VGGTLEAGFLALRRGWSINIGGGF--- 244
+ + + G + F R + GF
Sbjct: 127 AQRMFVMLPCGGVGVDTDTIWNELHSSNAARWAAGSVTDLAFKVASR----ELKNGFAVV 182
Query: 245 ----HHASETKGGGFCAYADISLLVKLLFQSKSISTAMIVDLDAHQGNGYEKDFMNETRI 300
HHA + GFC + +++ + L Q S +IVD D H GNG ++ F + +
Sbjct: 183 RPPGHHADHSTAMGFCFFNSVAIACRQLQQQSKASKILIVDWDVHHGNGTQQTFYQDPSV 242
Query: 301 FI-----METCI----TSKAKEA-----------IRCRIELAPYTEDQHYLEKIEAGLER 340
+ + E + L P D YL +
Sbjct: 243 LYISLHRHDDGNFFPGSGAVDEVGAGSGEGFNVNVAWAGGLDPPMGDPEYLAAFRIVVMP 302
Query: 341 SLRSFCPDIIVYNAGTDVLLND--PLGLLAISPQG 373
R F PD+++ +AG D PLG +S +
Sbjct: 303 IAREFSPDLVLVSAGFDAAEGHPAPLGGYHVSAKC 337
Score = 34.4 bits (79), Expect = 0.078
Identities = 14/41 (34%), Positives = 21/41 (51%)
Query: 26 HHASETKGGGFCAYADISLLVKLLFQSKSISTAMIVDLDAH 66
HHA + GFC + +++ + L Q S +IVD D H
Sbjct: 187 HHADHSTAMGFCFFNSVAIACRQLQQQSKASKILIVDWDVH 227
>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 = 38.7 bits (89), Expect = 0.004
Identities = 47/363 (12%), Positives = 106/363 (29%), Gaps = 107/363 (29%)
Query: 64 DAHQFSDYYFPSAHSIKRKRKVEFLKERKALEDEITSEPQ----------ESV----VTR 109
D F+ Y ++ R + L R+AL E+ ++ V
Sbjct: 122 DNQVFAKY------NVSRLQPYLKL--RQALL-ELRPAKNVLIDGVLGSGKTWVALDVCL 172
Query: 110 PWPIVYRPEYNVHFFKLEKLHPFDSKKWKHIFNYLWKHIFNYLVEAKFITQ----DNIIE 165
+ + + ++ + + L+ + ++ + L K Y ++ + ++ NI
Sbjct: 173 SYKVQCKMDFKIFWLNLKNCNSPET-----VLEMLQK--LLYQIDPNWTSRSDHSSNIKL 225
Query: 166 PQEVSEEQL--LIAHTEKYLKSL--------KW---SFNVAAISEVCP-LVAVPNYFVQK 211
+ +L L+ + Y L +FN++ C L+ V
Sbjct: 226 RIHSIQAELRRLLKS-KPYENCLLVLLNVQNAKAWNAFNLS-----CKILLTTRFKQVTD 279
Query: 212 CYLRPMRYHVGGTLEAGFLALRRGWSINIGGGFHHASETKGGGFCAYADISLLVKLLFQS 271
H+ +L+ + E K Y D L +
Sbjct: 280 FLSAATTTHI--SLD------------HHSMTLTP-DEVK-SLLLKYLDCRPQ-DLPREV 322
Query: 272 KSIS---TAMIVDLDAHQGNGYE--KDFMNETRIFIMETCITSKAKEAIRCRIELAPYTE 326
+ + ++I + ++ K + I+E+ + L P
Sbjct: 323 LTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNV-----------LEPAEY 371
Query: 327 DQHYLEKIEAGLERSLRSFCPDIIVYNAGTDVLLNDPLGLLAISPQGIIRRDELVFMKAR 386
+ + L F P + P LL++ +I+ D +V +
Sbjct: 372 RKMF---------DRLSVF-PP--------SAHI--PTILLSLIWFDVIKSDVMVVVNKL 411
Query: 387 ERR 389
+
Sbjct: 412 HKY 414
Score = 30.6 bits (68), Expect = 1.1
Identities = 28/158 (17%), Positives = 46/158 (29%), Gaps = 49/158 (31%)
Query: 40 ADIS--LLVKLLFQSKSISTAMIVD-------LDAHQFSDYYFPSAHSIKRKRKVEFLKE 90
A I LL + F ++V+ ++ S SI + KV+ L+
Sbjct: 385 AHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTI--SIPSIYLELKVK-LEN 441
Query: 91 RKALEDEITSEPQESVVTRPWPIVYRPEYNVHFFKLEKLHPFDSKKWKHIFNYLWKHIFN 150
AL I V YN+ K D ++ Y + HI +
Sbjct: 442 EYALHRSI--------VDH---------YNIP-----KTFDSDDLIPPYLDQYFYSHIGH 479
Query: 151 YLVEAKFITQDNIIEPQEVSEEQLLIAHTEKYLKSLKW 188
+L E E L +L ++
Sbjct: 480 HLKNI------------EHPERMTLF--RMVFL-DFRF 502
>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 = 36.9 bits (84), Expect = 0.004
Identities = 13/47 (27%), Positives = 19/47 (40%), Gaps = 19/47 (40%)
Query: 326 EDQHYLEKIEAGLERSLRSFCPDIIVYNAGTDVLLNDPLGLLAISPQ 372
E Q L+K++A SL+ + D +A P LAI
Sbjct: 18 EKQA-LKKLQA----SLKLYADD----SA--------P--ALAIKAT 45
>3rd5_A Mypaa.01249.C; ssgcid, structural genomics, seattle structural
genomics CEN infectious disease, oxidoreductase; HET:
EPE; 1.50A {Mycobacterium paratuberculosis}
Length = 291
Score = 32.2 bits (74), Expect = 0.24
Identities = 27/118 (22%), Positives = 40/118 (33%), Gaps = 45/118 (38%)
Query: 341 SLRSFCP-----DIIVYNAGTDVLLNDPLGLLAISPQGIIRRDELVF------------- 382
S+R F D+++ NAG ++ P L + G E
Sbjct: 76 SVRRFADGVSGADVLINNAG---IMAVPYAL---TVDGF----ESQIGTNHLGHFALTNL 125
Query: 383 ----MKARERRVPIVMLTSGGYLKQTARIIADSILNLADLGLISRPYNIWFIYYTSKT 436
+ R +V ++S + RI NL DL SR Y+ W Y SK
Sbjct: 126 LLPRLTDR-----VVTVSSMAH--WPGRI------NLEDLNWRSRRYSPWLAYSQSKL 170
>3k7x_A LIN0763 protein; Q92DQ0, LKR23, NESG, structural genomics, PSI-2,
protein structure initiative, northeast structural
genomics consortium; 1.89A {Listeria innocua}
Length = 349
Score = 29.6 bits (66), Expect = 2.2
Identities = 10/38 (26%), Positives = 15/38 (39%)
Query: 320 ELAPYTEDQHYLEKIEAGLERSLRSFCPDIIVYNAGTD 357
EL T++ YL+ SL+ D I + G
Sbjct: 224 ELYRITKEAIYLDTANKTAAISLKELTEDGIFKDEGNG 261
>3snk_A Response regulator CHEY-like protein; P-loop containing nucleoside
triphosphate hydrolases, struct genomics; 2.02A
{Mesorhizobium loti}
Length = 135
Score = 28.4 bits (64), Expect = 2.5
Identities = 11/85 (12%), Positives = 24/85 (28%), Gaps = 24/85 (28%)
Query: 335 EAGLERSLRSFCPDIIVYNAGTDVLLNDPLGLLAISPQGIIRRDELVFMKARERRVPIVM 394
+ P I++ D+ D LG I +A VP++
Sbjct: 49 DFLKGP-PADTRPGIVI----LDLGGGDLLGK------PGIVE-----ARALWATVPLIA 92
Query: 395 LTSGGYLKQTARIIADSILNLADLG 419
+ + + ++ L +
Sbjct: 93 V--------SDELTSEQTRVLVRMN 109
>2yzr_A Pyridoxal biosynthesis lyase PDXS; redox protein, pyridoxal
phosphate, structural genomi NPPSFA; 2.30A
{Methanocaldococcus jannaschii}
Length = 330
Score = 29.0 bits (64), Expect = 3.6
Identities = 11/46 (23%), Positives = 20/46 (43%)
Query: 354 AGTDVLLNDPLGLLAISPQGIIRRDELVFMKARERRVPIVMLTSGG 399
VL N+P+ + I E++ + R+P+V +GG
Sbjct: 205 LPATVLENEPIYEGFTLAEIIDGLYEVLLEVKKLGRLPVVNFAAGG 250
>3ea0_A ATPase, para family; alpha-beta-alpha sandwich, structural
genomics, PSI-2, prote structure initiative; HET: ATP;
2.20A {Chlorobium tepidum}
Length = 245
Score = 28.4 bits (64), Expect = 4.4
Identities = 6/62 (9%), Positives = 21/62 (33%)
Query: 352 YNAGTDVLLNDPLGLLAISPQGIIRRDELVFMKARERRVPIVMLTSGGYLKQTARIIADS 411
+ + + ++ ++ I +DE ++ ++ + L +T A
Sbjct: 182 ADTNSRITSDEIEKVIGRPISKRIPQDEDAMQESLLSGQSVLKVAPKSQLSKTIVDWALH 241
Query: 412 IL 413
+
Sbjct: 242 LN 243
>3grc_A Sensor protein, kinase; protein structure initiative II(PSI II),
NYSGXRC, 11025B, structural genomics; 2.21A {Polaromonas
SP}
Length = 140
Score = 27.2 bits (61), Expect = 6.8
Identities = 14/62 (22%), Positives = 24/62 (38%), Gaps = 14/62 (22%)
Query: 335 EAGLERSLRSFCPDIIVYNAGTDVLLNDPLGLLAISPQGIIRRDELVFMKARERRVPIVM 394
LE+ + + D+ L D G+ I +RRD R R + IV+
Sbjct: 40 AQALEQ-VARRPYAAMT----VDLNLPDQDGVSLIR---ALRRDS------RTRDLAIVV 85
Query: 395 LT 396
++
Sbjct: 86 VS 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
0.323 0.139 0.422
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: 6,927,258
Number of extensions: 425669
Number of successful extensions: 886
Number of sequences better than 10.0: 1
Number of HSP's gapped: 865
Number of HSP's successfully gapped: 36
Length of query: 436
Length of database: 6,701,793
Length adjustment: 96
Effective length of query: 340
Effective length of database: 4,021,377
Effective search space: 1367268180
Effective search space used: 1367268180
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 59 (26.6 bits)