RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy10341
(213 letters)
>4a69_A Histone deacetylase 3,; transcription, hydrolase; HET: I0P; 2.06A
{Homo sapiens}
Length = 376
Score = 165 bits (419), Expect = 8e-50
Identities = 66/111 (59%), Positives = 90/111 (81%)
Query: 41 LGQFSLTTKGHGECVKFVRDLNVPLLVLGGGGYTLRNVARCWTYETSLLVNEEISNDIPD 100
LG F+L+ +GHGECV++V+ N+PLLVLGGGGYT+RNVARCWTYETSLLV E IS ++P
Sbjct: 266 LGCFNLSIRGHGECVEYVKSFNIPLLVLGGGGYTVRNVARCWTYETSLLVEEAISEELPY 325
Query: 101 SLYKDFFQPDYNLHPEFVHKHDNANSKQYLELITKTVYDNLKMVAFSPSVQ 151
S Y ++F PD+ LHP+ + +N NS+QYL+ I +T+++NLKM+ +PSVQ
Sbjct: 326 SEYFEYFAPDFTLHPDVSTRIENQNSRQYLDQIRQTIFENLKMLNHAPSVQ 376
>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 = 160 bits (406), Expect = 8e-48
Identities = 36/113 (31%), Positives = 58/113 (51%), Gaps = 1/113 (0%)
Query: 41 LGQFSLTTKGHGECVKFVRDLNVPLLVLGGGGYTLRNVARCWTYETSLLVNEEISNDIPD 100
+ F++T G G+C+K++ + L+LGGGGY L N ARCWTY T +++ + +S++IPD
Sbjct: 274 MCSFNMTPVGIGKCLKYILQWQLATLILGGGGYNLANTARCWTYLTGVILGKTLSSEIPD 333
Query: 101 SLYKDFFQPDYNLHPEFVHKHDNANSKQYLELITKTVYDNLKMVAFSPSVQMQ 153
+ + PDY L + N ++ I + NLK V
Sbjct: 334 HEFFTAYGPDYVLEIT-PSCRPDRNEPHRIQQILNYIKGNLKHVVIEGRSHHH 385
>3max_A HD2, histone deacetylase 2; class 2, HDAC, foot pocket, hydrolase;
HET: LLX NHE; 2.05A {Homo sapiens}
Length = 367
Score = 145 bits (367), Expect = 3e-42
Identities = 51/104 (49%), Positives = 77/104 (74%), Gaps = 1/104 (0%)
Query: 41 LGQFSLTTKGHGECVKFVRDLNVPLLVLGGGGYTLRNVARCWTYETSLLVNEEISNDIPD 100
LG F+LT KGH +CV+ V+ N+PLL+LGGGGYT+RNVARCWTYET++ ++ EI N++P
Sbjct: 265 LGCFNLTVKGHAKCVEVVKTFNLPLLMLGGGGYTIRNVARCWTYETAVALDCEIPNELPY 324
Query: 101 SLYKDFFQPDYNLHPEFVHKHDNANSKQYLELITKTVYDNLKMV 144
+ Y ++F PD+ LH N N+ +Y+E I + +++NL+M+
Sbjct: 325 NDYFEYFGPDFKLHIS-PSNMTNQNTPEYMEKIKQRLFENLRML 367
>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 = 128 bits (323), Expect = 9e-36
Identities = 23/107 (21%), Positives = 41/107 (38%), Gaps = 3/107 (2%)
Query: 41 LGQFSLTTKGHGECVKFVRDLNVPLLVLGGGGYTLRNVARCWTYETSLLVNEEISNDIPD 100
L +F+L+ + VR++ + LGGGGY +AR WT L E+ + +
Sbjct: 265 LSKFNLSNVAFLKAFNIVREVFGEGVYLGGGGYHPYALARAWTLIWCELSGREVPEKLNN 324
Query: 101 SLYKDFFQPDYNLHPEFV---HKHDNANSKQYLELITKTVYDNLKMV 144
+ D+ + V + + + K V D L+
Sbjct: 325 KAKELLKSIDFEEFDDEVDRSYMLETLKDPWRGGEVRKEVKDTLEKA 371
>4dgw_C PRE-mRNA-splicing factor PRP11; zinc finger; 3.11A {Saccharomyces
cerevisiae}
Length = 231
Score = 41.6 bits (97), Expect = 6e-05
Identities = 18/113 (15%), Positives = 34/113 (30%), Gaps = 27/113 (23%)
Query: 91 NEEISNDIPDSLYKDFFQPDYNLHPEFVHKHDNANSKQYLELITKTVYDNLKMVAFS-PS 149
+ E+ + DS K P + K++L +I ++N +A P
Sbjct: 125 SSEVKENSVDSDDKAKVPPLIRIVSGLELSDTKQKGKKFL-VIAYEPFEN---IAIELPP 180
Query: 150 VQMQDMIGDVFTRDIGAVLDEMDPDIKNPQLEEDKRVDPANE---FYDGDNDQ 199
+E+ N + VD N+ F+D +
Sbjct: 181 -------------------NEILFSENNDMDNNNDGVDELNKKCTFWDAISKL 214
>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 = 0.001
Identities = 27/156 (17%), Positives = 53/156 (33%), Gaps = 21/156 (13%)
Query: 33 LLVLGGGGLGQFSLTTKGHGECVKFVRDLNVPLLVLGGGGYTLRNVARCWTYETSLLVNE 92
+L+ G G G+ + + V + + L N+ C + ET L + +
Sbjct: 153 VLIDGVLGSGKTWVA-------LDVCLSYKV-QCKMDFKIFWL-NLKNCNSPETVLEMLQ 203
Query: 93 EISNDI-PDSLYKDFFQPDYNLHPEFVHKHDNA--NSKQYLE--LITKTVYDNLKMVAFS 147
++ I P+ + + L + SK Y L+ V + AF+
Sbjct: 204 KLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFN 263
Query: 148 PSVQMQDMIGDVFTRDIGAVLDEMDPDI-KNPQLEE 182
S ++ + TR V D + + L+
Sbjct: 264 LSCKIL-----LTTRFKQ-VTDFLSAATTTHISLDH 293
Score = 32.5 bits (73), Expect = 0.10
Identities = 23/136 (16%), Positives = 42/136 (30%), Gaps = 36/136 (26%)
Query: 75 LRNVARCWTYETSLLV-----NEEISN--DIP--------DSLYKDFFQPDYNLHPEFVH 119
LR + + YE LLV N + N ++ DF H H
Sbjct: 234 LRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDH 293
Query: 120 KHDNANSKQYLELITKTV---YDNLK--MVAFSPSV------QMQDMIG----------D 158
+ L+ K + +L ++ +P ++D + D
Sbjct: 294 HSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCD 353
Query: 159 VFTRDIGAVLDEMDPD 174
T I + L+ ++P
Sbjct: 354 KLTTIIESSLNVLEPA 369
Score = 32.1 bits (72), Expect = 0.13
Identities = 17/117 (14%), Positives = 37/117 (31%), Gaps = 19/117 (16%)
Query: 103 YKDFFQPDYNLHPEFVHKHDNANSKQYL-ELITKTVYDNLKMVA---------F-----S 147
YKD FV D + + +++K D++ M F
Sbjct: 18 YKDILS---VFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTLRLFWTLLSK 74
Query: 148 PSVQMQDMIGDVFTRDIGAVLDEMDPDIKNPQLEEDKRVDPANEFYDGDNDQDAPDT 204
+Q + +V + ++ + + + P + ++ + Y DN A
Sbjct: 75 QEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLY-NDNQVFAKYN 130
Score = 29.4 bits (65), Expect = 1.1
Identities = 20/146 (13%), Positives = 40/146 (27%), Gaps = 52/146 (35%)
Query: 56 KFVRDLNVPLLVLGGGGYTLRNVARCWTYETSLLVNEEISNDI----------------- 98
FV + + ++V S+L EEI + I
Sbjct: 28 AFVDNFDC------------KDVQ---DMPKSILSKEEI-DHIIMSKDAVSGTLRLFWTL 71
Query: 99 ---PDSLYKDFF----QPDYNLHPEFVHKHDNA---NSKQYLELITKTVYDNLKMVAFSP 148
+ + + F + +Y + ++ Y+E + DN F+
Sbjct: 72 LSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDN---QVFAK 128
Query: 149 -SVQMQDMIGDVFTRDIGAVLDEMDP 173
+V + L E+ P
Sbjct: 129 YNVSRLQPY-----LKLRQALLELRP 149
Score = 28.7 bits (63), Expect = 1.8
Identities = 29/201 (14%), Positives = 65/201 (32%), Gaps = 57/201 (28%)
Query: 21 ECVKFVRDLNVPLLVLG--------------GGGLGQFSLTTKGHGECVKFVRDLNVPLL 66
F ++P ++L L ++SL K E + + + L
Sbjct: 377 RLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLELK 436
Query: 67 VLGGGGYTLR-------NVARCWTYETSLLVNEEISNDIPDSLYKDFFQPDYNLHPEFVH 119
V Y L N+ + + ++++ D Y F+ H H
Sbjct: 437 VKLENEYALHRSIVDHYNIPKTFD-------SDDLIPPYLDQ-Y--FYS-----H--IGH 479
Query: 120 KH-DNANSKQYLELITKTVYDNLKMV---------AFSPSVQMQDMIGDV-----FTRDI 164
H N + + L V+ + + + A++ S + + + + + D
Sbjct: 480 -HLKNIEHPERMTLFRM-VFLDFRFLEQKIRHDSTAWNASGSILNTLQQLKFYKPYICDN 537
Query: 165 GAVLDEMDPDIKN--PQLEED 183
+ + I + P++EE+
Sbjct: 538 DPKYERLVNAILDFLPKIEEN 558
>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 = 36.2 bits (83), Expect = 0.007
Identities = 21/158 (13%), Positives = 47/158 (29%), Gaps = 53/158 (33%)
Query: 76 RNVARCWTYETSLLVNEEISNDIPDSLYKDFFQPDYNLHPEFVHKHDNA----NSKQYL- 130
+ + + + ++ +L++ + + L F N+ Y
Sbjct: 120 KELIKNY-ITARIMAKRPFDKKSNSALFRAVGEGNAQLVAIF-------GGQGNTDDYFE 171
Query: 131 ELITKTVYDNLKMVAFSPSVQMQDMIGDVFTRDIGAVLDEMDPDIKNPQLEEDKRVDPAN 190
EL + +Y + ++GD+ L E+ +D
Sbjct: 172 EL--RDLYQ-----TYHV------LVGDLIKF-SAETLSELIRT----------TLDAEK 207
Query: 191 EFYDG-------DNDQDAPDTE------MSW---GLLQ 212
F G +N + PD + +S G++Q
Sbjct: 208 VFTQGLNILEWLENPSNTPDKDYLLSIPISCPLIGVIQ 245
Score = 30.8 bits (69), Expect = 0.38
Identities = 29/164 (17%), Positives = 46/164 (28%), Gaps = 81/164 (49%)
Query: 50 GH--GE-----C----------VKFVR------DLNVPLLVLGGGGY------------- 73
GH GE V+ V + VP LG Y
Sbjct: 1761 GHSLGEYAALASLADVMSIESLVEVVFYRGMTMQVAVPRDELGRSNYGMIAINPGRVAAS 1820
Query: 74 ----TLRNVARCWTYETSLLVNEEISNDIPDSLYKDFFQPDYNLHPEFVHKHDNANSKQY 129
L+ V T LV EI N N ++QY
Sbjct: 1821 FSQEALQYVVERVGKRTGWLV--EIVNY-------------------------NVENQQY 1853
Query: 130 --------LELITKTVYDNLK-----MVAFSPSVQMQDMIGDVF 160
L+ +T V + +K ++ S+ ++++ G +F
Sbjct: 1854 VAAGDLRALDTVTN-VLNFIKLQKIDIIELQKSLSLEEVEGHLF 1896
>3men_A Acetylpolyamine aminohydrolase; histone deacetylase; 2.20A
{Burkholderia pseudomallei 1710B}
Length = 362
Score = 33.6 bits (77), Expect = 0.038
Identities = 10/41 (24%), Positives = 20/41 (48%)
Query: 41 LGQFSLTTKGHGECVKFVRDLNVPLLVLGGGGYTLRNVARC 81
Q ++TT G G + L +P +++ GGY + ++
Sbjct: 309 QSQVAVTTDGFGRLGHLIGALRLPTVIVQEGGYHIESLEAN 349
Score = 27.8 bits (62), Expect = 3.0
Identities = 11/35 (31%), Positives = 16/35 (45%), Gaps = 1/35 (2%)
Query: 6 HDRLGQFSLTTKGHGECVKFVRDLNVPLL-VLGGG 39
D Q ++TT G G + L +P + V GG
Sbjct: 306 DDPQSQVAVTTDGFGRLGHLIGALRLPTVIVQEGG 340
>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 = 33.2 bits (76), Expect = 0.054
Identities = 11/41 (26%), Positives = 19/41 (46%)
Query: 41 LGQFSLTTKGHGECVKFVRDLNVPLLVLGGGGYTLRNVARC 81
+ F LT+ + + + VPLLV+ GGY + +
Sbjct: 291 ISFFKLTSPDYITMGRTIAASGVPLLVVMEGGYGVPEIGLN 331
Score = 27.0 bits (60), Expect = 5.0
Identities = 11/35 (31%), Positives = 17/35 (48%), Gaps = 1/35 (2%)
Query: 6 HDRLGQFSLTTKGHGECVKFVRDLNVPLL-VLGGG 39
D + F LT+ + + + VPLL V+ GG
Sbjct: 288 QDPISFFKLTSPDYITMGRTIAASGVPLLVVMEGG 322
>3i99_A UDP-N-acetylenolpyruvoylglucosamine reductase; structural
genomics, center for structural of infectious diseases,
csgid; HET: FAD; 2.20A {Vibrio cholerae}
Length = 357
Score = 28.0 bits (63), Expect = 2.3
Identities = 4/19 (21%), Positives = 8/19 (42%)
Query: 21 ECVKFVRDLNVPLLVLGGG 39
++P L++G G
Sbjct: 45 ALYCSAEWASLPKLIIGKG 63
Score = 28.0 bits (63), Expect = 2.3
Identities = 4/19 (21%), Positives = 8/19 (42%)
Query: 53 ECVKFVRDLNVPLLVLGGG 71
++P L++G G
Sbjct: 45 ALYCSAEWASLPKLIIGKG 63
>1uxy_A MURB, uridine diphospho-N-acetylenolpyruvylglucosamine reductase;
peptidoglycan synthesis, cell WALL, cell division,
oxidoreductase, NADP; HET: FAD EPU; 1.80A {Escherichia
coli} SCOP: d.145.1.2 d.146.1.1 PDB: 1mbb_A* 1mbt_A*
2q85_A* 2mbr_A*
Length = 340
Score = 27.9 bits (63), Expect = 2.5
Identities = 5/19 (26%), Positives = 9/19 (47%)
Query: 21 ECVKFVRDLNVPLLVLGGG 39
++ P+L+LG G
Sbjct: 29 NAWQYATAEGQPVLILGEG 47
Score = 27.9 bits (63), Expect = 2.5
Identities = 5/19 (26%), Positives = 9/19 (47%)
Query: 53 ECVKFVRDLNVPLLVLGGG 71
++ P+L+LG G
Sbjct: 29 NAWQYATAEGQPVLILGEG 47
>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 = 27.4 bits (61), Expect = 3.7
Identities = 8/42 (19%), Positives = 19/42 (45%), Gaps = 1/42 (2%)
Query: 41 LGQFSLTTKGHGECVKFVRDL-NVPLLVLGGGGYTLRNVARC 81
LG + ++ K G + + +L +++ GG+ L +
Sbjct: 328 LGGYHVSAKCFGYMTQQLMNLAGGAVVLALEGGHDLTAICDA 369
>2bvf_A 6-hydroxy-D-nicotine oxidase; autoflavinylation, enantiomeric
substrates, flavoenzymes, NI degradation; HET: FAD;
1.92A {Arthrobacter nicotinovorans} PDB: 2bvg_A*
2bvh_A*
Length = 459
Score = 27.0 bits (60), Expect = 5.1
Identities = 6/31 (19%), Positives = 13/31 (41%), Gaps = 1/31 (3%)
Query: 21 ECVKFVRDLNVPLLVLGGG-GLGQFSLTTKG 50
+ V++ D + + V GG ++ G
Sbjct: 53 KSVRYACDNGLEISVRSGGHNPNGYATNDGG 83
>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 = 26.3 bits (59), Expect = 7.3
Identities = 7/19 (36%), Positives = 10/19 (52%)
Query: 21 ECVKFVRDLNVPLLVLGGG 39
E V + +PL +LG G
Sbjct: 69 EVVAYCHQNKIPLTILGNG 87
Score = 26.3 bits (59), Expect = 7.3
Identities = 7/19 (36%), Positives = 10/19 (52%)
Query: 53 ECVKFVRDLNVPLLVLGGG 71
E V + +PL +LG G
Sbjct: 69 EVVAYCHQNKIPLTILGNG 87
>1hsk_A UDP-N-acetylenolpyruvoylglucosamine reductase; peptidoglycan
synthesis, cell WALL, cell division, oxidoreductase,
NADP, flavoprotein, FAD; HET: FAD; 2.30A
{Staphylococcus aureus} SCOP: d.145.1.2 d.146.1.1
Length = 326
Score = 26.0 bits (58), Expect = 9.8
Identities = 6/19 (31%), Positives = 9/19 (47%)
Query: 21 ECVKFVRDLNVPLLVLGGG 39
VK+ +P+ LG G
Sbjct: 63 AVVKYAYQNEIPVTYLGNG 81
Score = 26.0 bits (58), Expect = 9.8
Identities = 6/19 (31%), Positives = 9/19 (47%)
Query: 53 ECVKFVRDLNVPLLVLGGG 71
VK+ +P+ LG G
Sbjct: 63 AVVKYAYQNEIPVTYLGNG 81
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
0.318 0.139 0.427
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: 3,338,828
Number of extensions: 198689
Number of successful extensions: 458
Number of sequences better than 10.0: 1
Number of HSP's gapped: 454
Number of HSP's successfully gapped: 36
Length of query: 213
Length of database: 6,701,793
Length adjustment: 90
Effective length of query: 123
Effective length of database: 4,188,903
Effective search space: 515235069
Effective search space used: 515235069
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 55 (25.5 bits)