RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 014470
(424 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 = 622 bits (1607), Expect = 0.0
Identities = 154/383 (40%), Positives = 228/383 (59%), Gaps = 4/383 (1%)
Query: 9 PSGTDGVKRKVCYFYDPEVGNYYYGQGHPMKPHRIRMTHALLAHYGLLQNMQVLKPFPAR 68
G Y Y PE + P R M H+L+ Y L + M+++KP A
Sbjct: 6 EPADSGQSLVPVYIYSPEYVSM--CDSLAKIPKRASMVHSLIEAYALHKQMRIVKPKVAS 63
Query: 69 ERDLCRFHADDYVSFLRSITPETQQDQLRQLKRFNVGEDCPVFDGLFSFCQTYAGGSVGG 128
++ FH D Y+ L+ ++ E D + + +G CP +G+F + G ++
Sbjct: 64 MEEMATFHTDAYLQHLQKVSQEGDDDHPDSI-EYGLGYLCPATEGIFDYAAAIGGATITA 122
Query: 129 AVKLNHGLCDIAINWAGGLHHAKKCEASGFCYVNDIVLAILELLKQHERVLYVDIDIHHG 188
A L G+C +AINW+GG HHAKK EASGFCY+ND VL IL L ++ ER+LYVD+D+HHG
Sbjct: 123 AQCLIDGMCKVAINWSGGWHHAKKDEASGFCYLNDAVLGILRLRRKFERILYVDLDLHHG 182
Query: 189 DGVEEAFYTTDRVMTVSFHKFGD-YFPGTGDIRDIGYSKGKFYSLNVPLDDGIDDESYHY 247
DGVE+AF T +VMTVS HKF +FPGTGD+ D+G KG++YS+NVP+ DGI DE Y+
Sbjct: 183 DGVEDAFSFTSKVMTVSLHKFSPGFFPGTGDVSDVGLGKGRYYSVNVPIQDGIQDEKYYQ 242
Query: 248 LFKPIIGKVMEVFRPGAVVLQCGADSLSGDRLGCFNLSIKGHAECVKFMRSFNVPLLLLG 307
+ + ++ +V + F P AVVLQ GAD+++GD + FN++ G +C+K++ + + L+LG
Sbjct: 243 ICESVLKEVYQAFNPKAVVLQLGADTIAGDPMCSFNMTPVGIGKCLKYILQWQLATLILG 302
Query: 308 GGGYTIRNVARCWCYETGVALGVEVDDKMPQHEYYEYFGPDYTLHVAPSNMENKNSRQLL 367
GGGY + N ARCW Y TGV LG + ++P HE++ +GPDY L + PS ++N +
Sbjct: 303 GGGYNLANTARCWTYLTGVILGKTLSSEIPDHEFFTAYGPDYVLEITPSCRPDRNEPHRI 362
Query: 368 EEIRNKLLEYLSKLQHAPSVQFQ 390
++I N + L +
Sbjct: 363 QQILNYIKGNLKHVVIEGRSHHH 385
>3max_A HD2, histone deacetylase 2; class 2, HDAC, foot pocket, hydrolase;
HET: LLX NHE; 2.05A {Homo sapiens}
Length = 367
Score = 620 bits (1600), Expect = 0.0
Identities = 250/366 (68%), Positives = 312/366 (85%)
Query: 16 KRKVCYFYDPEVGNYYYGQGHPMKPHRIRMTHALLAHYGLLQNMQVLKPFPARERDLCRF 75
K+KVCY+YD ++GNYYYGQGHPMKPHRIRMTH LL +YGL + M++ +P A ++ ++
Sbjct: 2 KKKVCYYYDGDIGNYYYGQGHPMKPHRIRMTHNLLLNYGLYRKMEIYRPHKATAEEMTKY 61
Query: 76 HADDYVSFLRSITPETQQDQLRQLKRFNVGEDCPVFDGLFSFCQTYAGGSVGGAVKLNHG 135
H+D+Y+ FLRSI P+ + +Q++RFNVGEDCPVFDGLF FCQ GGSV GAVKLN
Sbjct: 62 HSDEYIKFLRSIRPDNMSEYSKQMQRFNVGEDCPVFDGLFEFCQLSTGGSVAGAVKLNRQ 121
Query: 136 LCDIAINWAGGLHHAKKCEASGFCYVNDIVLAILELLKQHERVLYVDIDIHHGDGVEEAF 195
D+A+NWAGGLHHAKK EASGFCYVNDIVLAILELLK H+RVLY+DIDIHHGDGVEEAF
Sbjct: 122 QTDMAVNWAGGLHHAKKSEASGFCYVNDIVLAILELLKYHQRVLYIDIDIHHGDGVEEAF 181
Query: 196 YTTDRVMTVSFHKFGDYFPGTGDIRDIGYSKGKFYSLNVPLDDGIDDESYHYLFKPIIGK 255
YTTDRVMTVSFHK+G+YFPGTGD+RDIG KGK+Y++N P+ DGIDDESY +FKPII K
Sbjct: 182 YTTDRVMTVSFHKYGEYFPGTGDLRDIGAGKGKYYAVNFPMRDGIDDESYGQIFKPIISK 241
Query: 256 VMEVFRPGAVVLQCGADSLSGDRLGCFNLSIKGHAECVKFMRSFNVPLLLLGGGGYTIRN 315
VME+++P AVVLQCGADSLSGDRLGCFNL++KGHA+CV+ +++FN+PLL+LGGGGYTIRN
Sbjct: 242 VMEMYQPSAVVLQCGADSLSGDRLGCFNLTVKGHAKCVEVVKTFNLPLLMLGGGGYTIRN 301
Query: 316 VARCWCYETGVALGVEVDDKMPQHEYYEYFGPDYTLHVAPSNMENKNSRQLLEEIRNKLL 375
VARCW YET VAL E+ +++P ++Y+EYFGPD+ LH++PSNM N+N+ + +E+I+ +L
Sbjct: 302 VARCWTYETAVALDCEIPNELPYNDYFEYFGPDFKLHISPSNMTNQNTPEYMEKIKQRLF 361
Query: 376 EYLSKL 381
E L L
Sbjct: 362 ENLRML 367
>4a69_A Histone deacetylase 3,; transcription, hydrolase; HET: I0P; 2.06A
{Homo sapiens}
Length = 376
Score = 612 bits (1581), Expect = 0.0
Identities = 233/375 (62%), Positives = 299/375 (79%), Gaps = 2/375 (0%)
Query: 16 KRKVCYFYDPEVGNYYYGQGHPMKPHRIRMTHALLAHYGLLQNMQVLKPFPARERDLCRF 75
+ V YFYDP+VGN++YG GHPMKPHR+ +TH+L+ HYGL + M V KP+ A + D+CRF
Sbjct: 2 AKTVAYFYDPDVGNFHYGAGHPMKPHRLALTHSLVLHYGLYKKMIVFKPYQASQHDMCRF 61
Query: 76 HADDYVSFLRSITPETQQDQLRQLKRFNVGEDCPVFDGLFSFCQTYAGGSVGGAVKLNHG 135
H++DY+ FL+ ++P Q + L FNVG+DCPVF GLF FC Y G S+ GA +LN+
Sbjct: 62 HSEDYIDFLQRVSPTNMQGFTKSLNAFNVGDDCPVFPGLFEFCSRYTGASLQGATQLNNK 121
Query: 136 LCDIAINWAGGLHHAKKCEASGFCYVNDIVLAILELLKQHERVLYVDIDIHHGDGVEEAF 195
+CDIAINWAGGLHHAKK EASGFCYVNDIV+ ILELLK H RVLY+DIDIHHGDGV+EAF
Sbjct: 122 ICDIAINWAGGLHHAKKFEASGFCYVNDIVIGILELLKYHPRVLYIDIDIHHGDGVQEAF 181
Query: 196 YTTDRVMTVSFHKFGDY-FPGTGDIRDIGYSKGKFYSLNVPLDDGIDDESYHYLFKPIIG 254
Y TDRVMTVSFHK+G+Y FPGTGD+ ++G G++Y LNVPL DGIDD+SY +LF+P+I
Sbjct: 182 YLTDRVMTVSFHKYGNYFFPGTGDMYEVGAESGRYYCLNVPLRDGIDDQSYKHLFQPVIN 241
Query: 255 KVMEVFRPGAVVLQCGADSLSGDRLGCFNLSIKGHAECVKFMRSFNVPLLLLGGGGYTIR 314
+V++ ++P +VLQCGADSL DRLGCFNLSI+GH ECV++++SFN+PLL+LGGGGYT+R
Sbjct: 242 QVVDFYQPTCIVLQCGADSLGCDRLGCFNLSIRGHGECVEYVKSFNIPLLVLGGGGYTVR 301
Query: 315 NVARCWCYETGVALGVEVDDKMPQHEYYEYFGPDYTLHV-APSNMENKNSRQLLEEIRNK 373
NVARCW YET + + + +++P EY+EYF PD+TLH + +EN+NSRQ L++IR
Sbjct: 302 NVARCWTYETSLLVEEAISEELPYSEYFEYFAPDFTLHPDVSTRIENQNSRQYLDQIRQT 361
Query: 374 LLEYLSKLQHAPSVQ 388
+ E L L HAPSVQ
Sbjct: 362 IFENLKMLNHAPSVQ 376
>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 = 559 bits (1443), Expect = 0.0
Identities = 115/376 (30%), Positives = 181/376 (48%), Gaps = 11/376 (2%)
Query: 17 RKVCYFYDPEVGNYYYGQGHPMKPHRIRMTHALLAHYGLLQNMQVLKPFPARERDLCRFH 76
+KV + G Y Y + HP+K R+ + L+ +++K PA + +L FH
Sbjct: 2 KKVKLIGTLDYGKYRYPKNHPLKIPRVSLLLRFKDAMNLIDEKELIKSRPATKEELLLFH 61
Query: 77 ADDYVSFLRSITPETQQDQLRQLKRFNVG-EDCPVFDGLFSFCQTYAGGSVGGAVKLNHG 135
+DY++ L Q +++N+G + PV +F+ G +V + G
Sbjct: 62 TEDYINTLMEAERC-QCVPKGAREKYNIGGYENPVSYAMFTGSSLATGSTVQAIEEFLKG 120
Query: 136 LCDIAINWAGGLHHAKKCEASGFCYVNDIVLAILELLKQ-HERVLYVDIDIHHGDGVEEA 194
++A N AGG+HHA K A+GFCY+N+ + I L K+ +R+LY+D+D HH DGV+EA
Sbjct: 121 --NVAFNPAGGMHHAFKSRANGFCYINNPAVGIEYLRKKGFKRILYIDLDAHHCDGVQEA 178
Query: 195 FYTTDRVMTVSFHKFGDYF--PGTGDIRDIGYSKGKFYSLNVPLDDGIDDESYHYLFKPI 252
FY TD+V +S H+ +Y G + +IG KGK Y+LN+PL G++D + + +
Sbjct: 179 FYDTDQVFVLSLHQSPEYAFPFEKGFLEEIGEGKGKGYNLNIPLPKGLNDNEFLFALEKS 238
Query: 253 IGKVMEVFRPGAVVLQCGADSLSGDRLGCFNLSIKGHAECVKFMRSFNVPLLLLGGGGYT 312
+ V EVF P +LQ G D L D L FNLS + +R + LGGGGY
Sbjct: 239 LEIVKEVFEPEVYLLQLGTDPLLEDYLSKFNLSNVAFLKAFNIVREVFGEGVYLGGGGYH 298
Query: 313 IRNVARCWCYETGVALGVEVDDKMPQHEYYEYFGPDYTLHVA----PSNMENKNSRQLLE 368
+AR W G EV +K+ D+ +E
Sbjct: 299 PYALARAWTLIWCELSGREVPEKLNNKAKELLKSIDFEEFDDEVDRSYMLETLKDPWRGG 358
Query: 369 EIRNKLLEYLSKLQHA 384
E+R ++ + L K + +
Sbjct: 359 EVRKEVKDTLEKAKAS 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 = 173 bits (440), Expect = 3e-50
Identities = 75/364 (20%), Positives = 139/364 (38%), Gaps = 30/364 (8%)
Query: 22 FYDPEVGNYYYGQGHPMKPHRIRMTHALLAHYGLLQNMQVLKPFPARERDLCRFHADDYV 81
H P R H L+ G ++++ + A + D+ R H+ ++
Sbjct: 22 AAANLTARMQPISHHLAHPDTKRRFHELVCASGQIEHLTPIAAVAATDADILRAHSAAHL 81
Query: 82 SFLRSITPETQQDQLRQLKRFNVGEDCPVFDGLFSFCQTY--AGGSVGGAVKLNHGLCDI 139
++ ++ + +G A S GGAV+L +
Sbjct: 82 ENMKRVSNLPTG-------GDTGDGITMMGNG------GLEIARLSAGGAVELTRRVATG 128
Query: 140 AINWAGGL-----HHAKKCEASGFCYVNDIVLAILELLKQH--ERVLYVDIDIHHGDGVE 192
++ L HHA A GFC N+ +A ERV +D D+HHG+G +
Sbjct: 129 ELSAGYALVNPPGHHAPHNAAMGFCIFNNTSVAAGYARAVLGMERVAILDWDVHHGNGTQ 188
Query: 193 EAFYTTDRVMTVSFHKFGDYFPGTGDIRDIGYSKGKFYSLNVPLDDGIDDESYHYLFKPI 252
+ ++ V+T+S H+ + P +G + G G Y++NVPL G + +Y + +
Sbjct: 189 DIWWNDPSVLTISLHQHLCFPPDSGYSTERGAGNGHGYNINVPLPPGSGNAAYLHAMDQV 248
Query: 253 IGKVMEVFRPGAVVLQCGADSLSGDRLGCFNLSIKGHAECVKFMRSF-----NVPLLLLG 307
+ + +RP +++ G D+ D L ++ G + + + ++ +
Sbjct: 249 VLPALRAYRPQLIIVGSGFDASMLDPLARMMVTADGFRQMARRTIDCAADICDGRIVFVQ 308
Query: 308 GGGYTIRNVARCWCYETGVALGVEVDDKMPQHEYYEYFGPDYTLHVAPSNMENKNSRQLL 367
GGY+ + C GV P HE+ G + L + +E LL
Sbjct: 309 EGGYSPHYLPFCGLAVIEELTGVR-SLPDPYHEFLAGMGGNTLLDAERAAIE--EIVPLL 365
Query: 368 EEIR 371
+IR
Sbjct: 366 ADIR 369
>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 = 171 bits (436), Expect = 2e-49
Identities = 84/412 (20%), Positives = 156/412 (37%), Gaps = 46/412 (11%)
Query: 6 NSLPSGTDGVKRKVCYFYDPE----VGNYYYGQGHPMKPHRIRMTHALLAHYGLLQNMQV 61
+S + + YD + HP RI+ + L GL +
Sbjct: 25 SSSETPARTLPFTTGLIYDSVMLKHQCSCGDNSRHPEHAGRIQSIWSRLQERGLRSQCEC 84
Query: 62 LKPFPARERDLCRFHADDYVSFLRSITPETQQDQLRQLKRFNVGEDCPV---------FD 112
L+ A +L H++ +V + + +L + D
Sbjct: 85 LRGRKASLEELQSVHSERHVLLYGTNPLSRLKLDNGKLAGLLAQRMFVMLPCGGVGVDTD 144
Query: 113 GLFSFCQTY--AGGSVGGAVKLNHGLCDIAINWAGGL-----HHAKKCEASGFCYVNDIV 165
+++ + A + G L + + + HHA A GFC+ N +
Sbjct: 145 TIWNELHSSNAARWAAGSVTDLAFKVASRELKNGFAVVRPPGHHADHSTAMGFCFFNSVA 204
Query: 166 LAILELLKQH--ERVLYVDIDIHHGDGVEEAFYTTDRVMTVSFHKF--GDYFPGTGDIRD 221
+A +L +Q ++L VD D+HHG+G ++ FY V+ +S H+ G++FPG+G + +
Sbjct: 205 IACRQLQQQSKASKILIVDWDVHHGNGTQQTFYQDPSVLYISLHRHDDGNFFPGSGAVDE 264
Query: 222 IGYSKGKFYSLNVPL----DDGIDDESYHYLFKPIIGKVMEVFRPGAVVLQCGADSLSGD 277
+G G+ +++NV D + D Y F+ ++ + F P V++ G D+ G
Sbjct: 265 VGAGSGEGFNVNVAWAGGLDPPMGDPEYLAAFRIVVMPIAREFSPDLVLVSAGFDAAEGH 324
Query: 278 R--LGCFNLSIKGHAECVKFMRSF-NVPLLLLGGGGYTIRNVARCWCYETGVALGVEVDD 334
LG +++S K + + + ++L GG+ + + LG VD
Sbjct: 325 PAPLGGYHVSAKCFGYMTQQLMNLAGGAVVLALEGGHDLTAICDASEACVAALLGNRVD- 383
Query: 335 KMPQHEYYEYFGPDYTLHVAPSNMENKNSRQLLEEIRNKLLEYLSKLQHAPS 386
P E P N N+ + LE + +Y +Q S
Sbjct: 384 --PLSEEGWKQKP------------NLNAIRSLEAVIRVHSKYWGCMQRLAS 421
>3men_A Acetylpolyamine aminohydrolase; histone deacetylase; 2.20A
{Burkholderia pseudomallei 1710B}
Length = 362
Score = 168 bits (427), Expect = 2e-48
Identities = 68/336 (20%), Positives = 116/336 (34%), Gaps = 37/336 (11%)
Query: 16 KRKVCYFYDPE----VGNYYYGQG----HPMKPHRIRMTHALLAHYGLLQNMQVLKPFPA 67
+ ++ P+ Y+ +G P R A G V +P
Sbjct: 19 PGSMLTYFHPDQSLHHPRTYFSRGRMRMPQEVPERAARLVAAAFAMGF----PVREPDDF 74
Query: 68 RERDLCRFHADDYVSFLRSITPETQQDQLRQLKRFNVGEDCPVFDGLFSFCQTYAGGSVG 127
+ H Y+ FL ++ E + + L A
Sbjct: 75 GIAPIAAVHDTHYLRFLETVHREWKAMPEDWGDEAMSNIFVREPNALRGVLAQAARHLAD 134
Query: 128 GAVKLNHGLCDIAINWAGGL----------------------HHAKKCEASGFCYVNDIV 165
G+ + A A HHA+ A GFCY+N+
Sbjct: 135 GSCPVGEHTWRAAYWSAQSALAAAAAVRDGAPAAYALCRPPGHHARVDAAGGFCYLNNAA 194
Query: 166 LAILELLKQHERVLYVDIDIHHGDGVEEAFYTTDRVMTVSFHKFGD--YFPGTGDIRDIG 223
+A L +H RV +D D+HHG G++E FY V+ VS H Y G + G
Sbjct: 195 IAAQALRARHARVAVLDTDMHHGQGIQEIFYARRDVLYVSIHGDPTNFYPAVAGFDDERG 254
Query: 224 YSKGKFYSLNVPLDDGIDDESYHYLFKPIIGKVMEVFRPGAVVLQCGADSLSGDRLGCFN 283
+G Y++N+P+ G + ++ + + + F P A+VL G D D
Sbjct: 255 AGEGLGYNVNLPMPHGSSEAAFFERVDDAL-RELRRFAPDALVLSLGFDVYRDDPQSQVA 313
Query: 284 LSIKGHAECVKFMRSFNVPLLLLGGGGYTIRNVARC 319
++ G + + +P +++ GGY I ++
Sbjct: 314 VTTDGFGRLGHLIGALRLPTVIVQEGGYHIESLEAN 349
>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 = 158 bits (401), Expect = 6e-45
Identities = 55/313 (17%), Positives = 106/313 (33%), Gaps = 30/313 (9%)
Query: 33 GQGHPMKPHRIRMTHALLAHYGLLQNMQVLKPFPARERDLCRFHADDYVSFLRSITPETQ 92
P R A + G V+ P + + H Y++FL + +
Sbjct: 23 LVPPFEAPFRAEWILAAVKEAGF---DDVVAPARHGLETVLKVHDAGYLNFLETAWDRWK 79
Query: 93 QDQLRQLKRFNVGEDCPVFDGLFSFCQTYAGG-SVGGAVKLNHGLCDIAINWAGGL---- 147
+ + + + G ++ G + A++
Sbjct: 80 AAGYKGEAIATSFPVRRTSPRIPTDIEGQIGYYCNAAETAISPGTWEAALSSMASAIDGA 139
Query: 148 ------------------HHAKKCEASGFCYVNDIVLAILELLKQH-ERVLYVDIDIHHG 188
HHA G+C++N+ +A LL + +++ +D+D HHG
Sbjct: 140 DLIAAGHKAAFSLCRPPGHHAGIDMFGGYCFINNAAVAAQRLLDKGAKKIAILDVDFHHG 199
Query: 189 DGVEEAFYTTDRVMTVSFHKF--GDYFPGTGDIRDIGYSKGKFYSLNVPLDDGIDDESYH 246
+G ++ FY V S H + G + G G + N P+ G +
Sbjct: 200 NGTQDIFYERGDVFFASLHGDPAEAFPHFLGYAEETGKGAGAGTTANYPMGRGTPYSVWG 259
Query: 247 YLFKPIIGKVMEVFRPGAVVLQCGADSLSGDRLGCFNLSIKGHAECVKFMRSFNVPLLLL 306
+ K + F A+V+ G D+ D + F L+ + + + + VPLL++
Sbjct: 260 EALTDSL-KRIAAFGAEAIVVSLGVDTFEQDPISFFKLTSPDYITMGRTIAASGVPLLVV 318
Query: 307 GGGGYTIRNVARC 319
GGY + +
Sbjct: 319 MEGGYGVPEIGLN 331
>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 = 42.3 bits (99), Expect = 3e-04
Identities = 30/246 (12%), Positives = 57/246 (23%), Gaps = 92/246 (37%)
Query: 7 SLPSGTDGVKRKVCYFYDPEVGNYYYGQGHPMKPHRIRMTHALLAH--------YGL--- 55
L D K + NY + +P + AL +
Sbjct: 107 KLLQENDTTLVKTKEL----IKNYITARIMAKRPFDKKSNSALFRAVGEGNAQLVAIFGG 162
Query: 56 ----------LQNM----------------QVLKPFPARERDLCRFHAD--DYVSFLRSI 87
L+++ + L D + + + +L
Sbjct: 163 QGNTDDYFEELRDLYQTYHVLVGDLIKFSAETLSELIRTTLDAEKVFTQGLNILEWLE-- 220
Query: 88 TPETQ--QDQLRQLKRFNVGEDCPV---FDGLFSFCQTYAGGSVGGAVKLNHGLCDIAIN 142
P +D L P+ G+ + G G ++
Sbjct: 221 NPSNTPDKDYLLS---------IPISCPLIGVIQLAHYVVTAKLLG---FTPG--ELRSY 266
Query: 143 WAGGLHHAKKCEASGFCYVNDIVLAILELLKQHERVLYVDIDIHHGDGVEEAFYT-TDRV 201
G H++ +V A+ I D E+F+ +
Sbjct: 267 LKGATGHSQ-----------GLVTAVA---------------IAETDS-WESFFVSVRKA 299
Query: 202 MTVSFH 207
+TV F
Sbjct: 300 ITVLFF 305
Score = 30.8 bits (69), Expect = 1.3
Identities = 50/276 (18%), Positives = 77/276 (27%), Gaps = 113/276 (40%)
Query: 1 MDTGGNSLPSGTDGVKRKVCYFYDPEVGNYYYGQGHPMKPHRIRMTH-ALLAHYGLLQNM 59
DT G S+ D V +P ++G K RIR + A++ + +
Sbjct: 1654 KDTYGFSI---LDIVIN------NPVNLTIHFG---GEKGKRIRENYSAMIFETIVDGKL 1701
Query: 60 QVLKPFPARERDL--CRFHADDYVSFLRSITPETQ-------QDQLRQLKRFNVGEDCPV 110
+ K F F ++ L S T TQ + LK
Sbjct: 1702 KTEKIFKEINEHSTSYTFRSEK--GLL-SATQFTQPALTLMEKAAFEDLKS--------- 1749
Query: 111 FDGLFSFCQTYAGGSVG---------G------AVKL--------------------NHG 135
GL T+AG S+G V++ N+G
Sbjct: 1750 -KGLIPADATFAGHSLGEYAALASLADVMSIESLVEVVFYRGMTMQVAVPRDELGRSNYG 1808
Query: 136 LCDIAIN----WAGGLHHAKK------CEASG-FCY-VND------IVLA---------- 167
+ AIN A A + + +G VN V A
Sbjct: 1809 MI--AINPGRVAASFSQEALQYVVERVGKRTGWLVEIVNYNVENQQYVAAGDLRALDTVT 1866
Query: 168 -ILELLKQHERVLYVDIDI------HHGDGVEEAFY 196
+L +K + IDI + VE +
Sbjct: 1867 NVLNFIKLQK------IDIIELQKSLSLEEVEGHLF 1896
>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 = 41.4 bits (96), Expect = 5e-04
Identities = 56/422 (13%), Positives = 106/422 (25%), Gaps = 131/422 (31%)
Query: 39 KPHRIRMTHALLAHYGLL---QNMQVLKPFPARERDL-CRF---HADDYVSFLRSITPET 91
KP+ + LL +L QN + F +L C+ V+ S T
Sbjct: 241 KPYE----NCLL----VLLNVQNAKAWNAF-----NLSCKILLTTRFKQVTDFLSAATTT 287
Query: 92 QQDQLRQLKRFNVGEDCPVFDGLFSFCQTYAGGSVGGAVKLNHGLCDI---AINWAGGLH 148
E L Y L + ++
Sbjct: 288 HISLDHHSMTLTPDEV----KSLLL---KYLDCRPQ---DLPREVLTTNPRRLSIIAESI 337
Query: 149 HAKKCEASGFCYVN-----DIVLAILELLKQHE-RVLYVDIDIHHGDGV----------- 191
+ +VN I+ + L +L+ E R ++ + +
Sbjct: 338 RDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFP-PSAHIPTILLSLIW 396
Query: 192 EEAFYTTDRVMTVSFHKFG----DYFPGTGDIRDI--------------------GYSKG 227
+ + V+ HK+ T I I Y+
Sbjct: 397 FDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIP 456
Query: 228 KFYSLNVPLDDGIDDESYHYLFKPIIGKVMEVFRPGAVVLQCGADSLSGDRLGCFNLSIK 287
K + + + +D Y + IG +L
Sbjct: 457 KTFDSDDLIPPYLDQYFYSH-----IG---------------------------HHLKNI 484
Query: 288 GHAECVKFMRSFNVPLLLLGGGGYTIRNVARCWCYETGVALGVEVDDKMPQHEYYE-YFG 346
H E + R + L IR+ + W + + + Q ++Y+ Y
Sbjct: 485 EHPERMTLFRMVFLDFRFLEQ---KIRHDSTAWNASGSIL------NTLQQLKFYKPYIC 535
Query: 347 PDYTLHVAPSNMENKNSRQLLEEIRNKLLEYLSKLQHAPS---VQFQERPPDSELPEADE 403
+ + K R L+ I + L + L + ++ D + E
Sbjct: 536 DN----------DPKYER-LVNAILDFLPKIEENLICSKYTDLLRIALMAEDEAIFEEAH 584
Query: 404 DQ 405
Q
Sbjct: 585 KQ 586
Score = 40.6 bits (94), Expect = 0.001
Identities = 36/285 (12%), Positives = 77/285 (27%), Gaps = 65/285 (22%)
Query: 136 LC-DIAINWAGGLHHAKKCEASGFCYVNDIVLAILELL--KQHERVLYV-DIDIHHGDGV 191
L I NW H+ + ++ I + LL K +E L V ++ +
Sbjct: 205 LLYQIDPNWTSRSDHSSNIKLR----IHSIQAELRRLLKSKPYENCLLVLL-NVQNAKAW 259
Query: 192 EEAFYTTDRVMTVSFHKFGDYFPGTGDIRDIGYSKGKFYSLNVPLDDGIDDESYHYLFKP 251
AF + +++ + K + + SL+ DE
Sbjct: 260 N-AFNLSCKILLTTRFK--------QVTDFLSAATTTHISLDHHSMTLTPDEV------- 303
Query: 252 IIGKVMEVFRPGAVVLQCGADSLSGDRLGCFNLSIKGHAECVKFMRSFNVPLLLLGGGGY 311
+ L C L + L + AE ++ +
Sbjct: 304 -----KSLL---LKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLA------------- 342
Query: 312 TIRNVAR--CWCYETGVALGVEVDDKMPQHEYYEYFG--------PDYTLHVAPSNMENK 361
T N C T + + V + + ++ P L + ++
Sbjct: 343 TWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKS 402
Query: 362 NSRQLLEEIRNKLL------EYLSKLQHAPSVQFQERPPDSELPE 400
+ ++ ++ L E + PS+ + +
Sbjct: 403 DVMVVVNKLHKYSLVEKQPKESTISI---PSIYLELKVKLENEYA 444
Score = 34.1 bits (77), Expect = 0.12
Identities = 39/185 (21%), Positives = 58/185 (31%), Gaps = 66/185 (35%)
Query: 41 HRIRMTHALLAHYGLLQNMQVLKPFPARERDLCRFHADDYV-SF----LRSITPETQQDQ 95
HR ++ HY + K F DL + D Y S L++I +
Sbjct: 446 HRS-----IVDHY------NIPKTFD--SDDLIPPYLDQYFYSHIGHHLKNIEHPERMTL 492
Query: 96 LRQLKRFNVGEDCPVFDGLFSFCQTYAGGSVGGAVKLNHGLCDIAINWAGG----LHHAK 151
R + F D F F + K+ H A N +G L K
Sbjct: 493 FRMV--F--------LD--FRFLE----------QKIRHD--STAWNASGSILNTLQQLK 528
Query: 152 KCEASGFCYVND-------IVLAILELLKQHERVLYVD--IDI------HHGDGV-EEAF 195
+ Y+ D +V AIL+ L + E L D+ + + EEA
Sbjct: 529 FYKP----YICDNDPKYERLVNAILDFLPKIEENLICSKYTDLLRIALMAEDEAIFEEAH 584
Query: 196 YTTDR 200
R
Sbjct: 585 KQVQR 589
Score = 29.1 bits (64), Expect = 3.9
Identities = 14/69 (20%), Positives = 21/69 (30%), Gaps = 9/69 (13%)
Query: 320 WCYETGVALGVEVDDK-MPQHEYYEYFGPDYTLHVAPSNMENKNSRQLLEEIRNKLLEYL 378
+ + E M Y E Y N + Q ++R LLE
Sbjct: 93 FLMS---PIKTEQRQPSMMTRMYIEQRDRLYN-DNQVFAKYNVSRLQPYLKLRQALLE-- 146
Query: 379 SKLQHAPSV 387
L+ A +V
Sbjct: 147 --LRPAKNV 153
>2rf4_A DNA-directed RNA polymerase I subunit RPA4; transferase DNA/RNA,
DNA-binding, phosphorylation, POL I, POLI, rpoli,
nuclear protein; 3.10A {Saccharomyces cerevisiae}
Length = 214
Score = 31.2 bits (70), Expect = 0.42
Identities = 11/41 (26%), Positives = 18/41 (43%), Gaps = 5/41 (12%)
Query: 247 YLFKPIIGKVMEVFRPGAVVLQCGADSLSGDRLGCFNLSIK 287
Y+++P +G V+E + A + FN SIK
Sbjct: 123 YVWQPQVGDVLE-----GYIFIQSASHIGLLIHDAFNASIK 158
>1jad_A PLC-beta, phospholipase C beta; alpha helical coiled coil,
hydrolase; 2.40A {Meleagris gallopavo} SCOP: h.4.10.1
Length = 251
Score = 30.2 bits (67), Expect = 1.1
Identities = 8/34 (23%), Positives = 14/34 (41%)
Query: 67 ARERDLCRFHADDYVSFLRSITPETQQDQLRQLK 100
R HA + + + + E Q +L+ LK
Sbjct: 96 DGIRRRKEQHATEQTAKITELAREKQIAELKALK 129
>3mbh_A Putative phosphomethylpyrimidine kinase; structural genomics, joint
center for structural genomics, J protein structure
initiative; HET: MSE PXL; 2.00A {Bacteroides
thetaiotaomicron} PDB: 3mbj_A*
Length = 291
Score = 29.5 bits (67), Expect = 1.9
Identities = 10/36 (27%), Positives = 14/36 (38%)
Query: 184 DIHHGDGVEEAFYTTDRVMTVSFHKFGDYFPGTGDI 219
D H V +R V+ ++PGTGD
Sbjct: 191 DEPHKTSVYAYNRQGNRYWKVTCPYLPAHYPGTGDT 226
>3h74_A Pyridoxal kinase; PSI-II, structural genomics, prote structure
initiative, NEW YORK SGX research center for STRU
genomics, nysgxrc; 1.30A {Lactobacillus plantarum} PDB:
3hyo_A* 3ibq_A*
Length = 282
Score = 29.1 bits (66), Expect = 2.9
Identities = 13/58 (22%), Positives = 21/58 (36%), Gaps = 3/58 (5%)
Query: 163 DIVLAILELLKQHERVLYVDIDIHHGDGVEEAFYT-TDRVMTVSFHKFGDYFPGTGDI 219
I+ A+ LK V D+ D + A+ V + ++ GTGD
Sbjct: 161 VILPALQAQLKTGAHA--VITDVQRADQIGCAWLDEAGHVQYCGARRLPGHYNGTGDT 216
>3nz3_A SPR1345 protein, putative uncharacterized protein; all beta sheets,
IG-like fold, mucin-binding, mucin, cell SU cell
adhesion; HET: PGE; 2.00A {Streptococcus pneumoniae}
Length = 112
Score = 27.6 bits (61), Expect = 3.1
Identities = 8/57 (14%), Positives = 16/57 (28%), Gaps = 2/57 (3%)
Query: 183 IDIHHGDGVEEAFYTTDRVMTVSFHKFGDYFPGTGDIRDIGYSKGKFYSLNVPLDDG 239
I + D V V+ + TG + ++ G + + D
Sbjct: 26 IHYVDKVTNQNV--KEDVVQPVTLSRTKTENKVTGVVTYGEWTTGNWDEVISGKIDK 80
>1g9r_A Glycosyl transferase; alpha-beta structure; HET: UPF; 2.00A
{Neisseria meningitidis} SCOP: c.68.1.4 PDB: 1ga8_A*
1ss9_A*
Length = 311
Score = 28.2 bits (63), Expect = 4.6
Identities = 8/20 (40%), Positives = 14/20 (70%)
Query: 166 LAILELLKQHERVLYVDIDI 185
L + E + ++VLY+DID+
Sbjct: 87 LKLGEYIADCDKVLYLDIDV 106
>2hq2_A Putative heme/hemoglobin transport protein; heme oxygenase,
structural repeat; HET: HEM; 1.45A {Escherichia coli}
SCOP: e.62.1.1 PDB: 1u9t_A
Length = 354
Score = 28.0 bits (62), Expect = 6.5
Identities = 21/170 (12%), Positives = 53/170 (31%), Gaps = 34/170 (20%)
Query: 251 PIIGKVMEVFRPGAVVLQCGADSLSGDRLGCF-NLSIKGHAECVKFMRSFNVPLLLLGGG 309
+G+ + R V + ++G F N + GHA L+L
Sbjct: 69 ESVGETKCICRNEYAVHE---------QVGTFTNQHLNGHA------------GLILNPR 107
Query: 310 GYTIRNVARCWCYETGVALGVEVDDKMPQHEYYEYFGPDYTLHVAPSNMENKNSRQLLEE 369
+R W ++ + + + ++F + +N +
Sbjct: 108 ALDLRLFLNQWAS----VFHIKENTARGERQSIQFFDHQGDALLKVYATDNTDMAAW--- 160
Query: 370 IRNKLLEYLSKLQHAPSVQFQERPPDSELPEADEDQEDGDERWDPDSDMD 419
++LL + + + + D+ + + D ++ W +D+
Sbjct: 161 --SELLA---RFITDENTPLELKAVDAPVVQTRADATVVEQEWRAMTDVH 205
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
0.321 0.141 0.445
Gapped
Lambda K H
0.267 0.0515 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 7,160,760
Number of extensions: 456920
Number of successful extensions: 1228
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1199
Number of HSP's successfully gapped: 31
Length of query: 424
Length of database: 6,701,793
Length adjustment: 96
Effective length of query: 328
Effective length of database: 4,021,377
Effective search space: 1319011656
Effective search space used: 1319011656
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 (27.0 bits)