RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 048339
(386 letters)
>1zz1_A Histone deacetylase-like amidohydrolase; HET: SHH; 1.57A
{Alcaligenaceae bacterium} PDB: 1zz0_A* 1zz3_A* 2gh6_A*
2vcg_A*
Length = 369
Score = 366 bits (941), Expect = e-126
Identities = 108/369 (29%), Positives = 175/369 (47%), Gaps = 10/369 (2%)
Query: 20 FWDDGMLNHDTGKGLFDTGFDPGFLEVLEKHPENSDRIKNIVSILKRGPISPYISWHSGI 79
W+ DTG G ++ + H + D + ++ +++ + +
Sbjct: 6 VWNTLYGWVDTGTGSLAAANLTARMQPISHHLAHPDTKRRFHELVCASGQIEHLTPIAAV 65
Query: 80 PAQIPQLLSFHTPDYINELVEAD--KAGGKMVCDGTVLNPGSWGAALLAVGTTLSAMKHV 137
A +L H+ ++ + GG T++ G A L+ G + + V
Sbjct: 66 AATDADILRAHSAAHLENMKRVSNLPTGGDTGDGITMMGNGGLEIARLSAGGAVELTRRV 125
Query: 138 LDGHGKIAYALVRPPGHHAQPTMADGYCFLNNAGLAVQLALNS-GCGKVVVIDIDVHYGN 196
G YALV PPGHHA A G+C NN +A A G +V ++D DVH+GN
Sbjct: 126 ATGELSAGYALVNPPGHHAPHNAAMGFCIFNNTSVAAGYARAVLGMERVAILDWDVHHGN 185
Query: 197 GTAEGFYRSNKVLTISLHMNHGSWGPSHPQNGTVDELGEGEGFGYNLNIPLPNGTGDRGY 256
GT + ++ VLTISLH H + P +G E G G G GYN+N+PLP G+G+ Y
Sbjct: 186 GTQDIWWNDPSVLTISLH-QHLCF---PPDSGYSTERGAGNGHGYNINVPLPPGSGNAAY 241
Query: 257 VHAMTELVVPAIQKFEPNMIVLVVGQDSSAFDPNGRQCLTMDGYREMGRIVRSLADRYSG 316
+HAM ++V+PA++ + P +I++ G D+S DP R +T DG+R+M R A
Sbjct: 242 LHAMDQVVLPALRAYRPQLIIVGSGFDASMLDPLARMMVTADGFRQMARRTIDCAADICD 301
Query: 317 GRLLIVQEGGYHVTYSAYCLHATLEGVLNLPLALLSDPIAYYPEDEAFPVKVIESIKQYQ 376
GR++ VQEGGY Y +C A +E + + L DP + ++++ +
Sbjct: 302 GRIVFVQEGGYSPHYLPFCGLAVIEELTGVR--SLPDPYHEFLAGMG-GNTLLDAERAAI 358
Query: 377 NDVIPFLKG 385
+++P L
Sbjct: 359 EEIVPLLAD 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 = 297 bits (762), Expect = 1e-98
Identities = 87/341 (25%), Positives = 146/341 (42%), Gaps = 39/341 (11%)
Query: 19 VFWDDGMLNHDTGKGLFDTGFDPGFLEVLEKHPENSDRIKNIVSILKRGPISPYISWHSG 78
+ + K HP R+ ++ +
Sbjct: 6 LIGTLDYGKYRYPKN----------------HPLKIPRVSLLLRFKDAMNLIDEKELIKS 49
Query: 79 IPAQIPQLLSFHTPDYINELVEADKAGGKMVCD------GTVLNP---GSWGAALLAVGT 129
PA +LL FHT DYIN L+EA++ G NP + + LA G+
Sbjct: 50 RPATKEELLLFHTEDYINTLMEAERCQCVPKGAREKYNIGGYENPVSYAMFTGSSLATGS 109
Query: 130 TLSAMKHVLDGHGKIAYALVRPPG--HHAQPTMADGYCFLNNAGLAVQLALNSGCGKVVV 187
T+ A++ L G+ P G HHA + A+G+C++NN + ++ G +++
Sbjct: 110 TVQAIEEFLKGN-----VAFNPAGGMHHAFKSRANGFCYINNPAVGIEYLRKKGFKRILY 164
Query: 188 IDIDVHYGNGTAEGFYRSNKVLTISLHMNHGSWGPSHPQNGTVDELGEGEGFGYNLNIPL 247
ID+D H+ +G E FY +++V +SLH + P + G ++E+GEG+G GYNLNIPL
Sbjct: 165 IDLDAHHCDGVQEAFYDTDQVFVLSLHQSPEYAFP--FEKGFLEEIGEGKGKGYNLNIPL 222
Query: 248 PNGTGDRGYVHAMTELVVPAIQKFEPNMIVLVVGQDSSAFDPNGRQCLTMDGYREMGRIV 307
P G D ++ A+ + + + FEP + +L +G D D + L+ + + IV
Sbjct: 223 PKGLNDNEFLFALEKSLEIVKEVFEPEVYLLQLGTDPLLEDYLSKFNLSNVAFLKAFNIV 282
Query: 308 RSLADRYSGGRLLIVQEGGYHVTYSAYCLHATLEGVLNLPL 348
R + G + + GGYH A + +
Sbjct: 283 REVF-----GEGVYLGGGGYHPYALARAWTLIWCELSGREV 318
>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 = 287 bits (736), Expect = 2e-95
Identities = 98/358 (27%), Positives = 147/358 (41%), Gaps = 52/358 (14%)
Query: 19 VFWDDGMLNHDTGKGLFDTGFDPGFLEVLEKHPENSDRIKNIVSILKRGPISPYISWHSG 78
V + + + L+ P E R + I++ +K ++
Sbjct: 3 VIFSEDHKLRNAKTELYGGELVP--------PFEAPFRAEWILAAVKEAGFDDVVA---P 51
Query: 79 IPAQIPQLLSFHTPDYINELVEA--------------------------------DKAGG 106
+ +L H Y+N L A + G
Sbjct: 52 ARHGLETVLKVHDAGYLNFLETAWDRWKAAGYKGEAIATSFPVRRTSPRIPTDIEGQIGY 111
Query: 107 KMVCDGTVLNPGSWGAALLAVGTTLSAMKHVLDGHGKIAYALVRPPGHHAQPTMADGYCF 166
T ++PG+W AAL ++ + + + GH K A++L RPPGHHA M GYCF
Sbjct: 112 YCNAAETAISPGTWEAALSSMASAIDGADLIAAGH-KAAFSLCRPPGHHAGIDMFGGYCF 170
Query: 167 LNNAGLAVQLALNSGCGKVVVIDIDVHYGNGTAEGFYRSNKVLTISLHMNHGSWGPSHPQ 226
+NNA +A Q L+ G K+ ++D+D H+GNGT + FY V SLH + P
Sbjct: 171 INNAAVAAQRLLDKGAKKIAILDVDFHHGNGTQDIFYERGDVFFASLHGDPAEAFP--HF 228
Query: 227 NGTVDELGEGEGFGYNLNIPLPNGTGDRGYVHAMTELVVPAIQKFEPNMIVLVVGQDSSA 286
G +E G+G G G N P+ GT + A+T+ + I F IV+ +G D+
Sbjct: 229 LGYAEETGKGAGAGTTANYPMGRGTPYSVWGEALTD-SLKRIAAFGAEAIVVSLGVDTFE 287
Query: 287 FDPNGRQCLTMDGYREMGRIVRSLADRYSGGRLLIVQEGGYHVTYSAYCLHATLEGVL 344
DP LT Y MGR + + G LL+V EGGY V + L+GV
Sbjct: 288 QDPISFFKLTSPDYITMGRTIAAS-----GVPLLVVMEGGYGVPEIGLNVANVLKGVA 340
>3men_A Acetylpolyamine aminohydrolase; histone deacetylase; 2.20A
{Burkholderia pseudomallei 1710B}
Length = 362
Score = 277 bits (711), Expect = 3e-91
Identities = 88/357 (24%), Positives = 142/357 (39%), Gaps = 53/357 (14%)
Query: 19 VFWDDGMLNHDTGKGLFDTGFDPGFLEVLEKHPENSDRIKNIVSILKRGPISPYISWHSG 78
++ H E +R +V+
Sbjct: 24 TYFHPDQSLHHPRTYFSRGRMRM--------PQEVPERAARLVAAAFAMGFP----VREP 71
Query: 79 IPAQIPQLLSFHTPDYINELVEA-------------------------------DKAGGK 107
I + + H Y+ L +A
Sbjct: 72 DDFGIAPIAAVHDTHYLRFLETVHREWKAMPEDWGDEAMSNIFVREPNALRGVLAQAARH 131
Query: 108 MVCDGTVLNPGSWGAALLAVGTTLSAMKHVLDGHGKIAYALVRPPGHHAQPTMADGYCFL 167
+ + +W AA + + L+A V DG AYAL RPPGHHA+ A G+C+L
Sbjct: 132 LADGSCPVGEHTWRAAYWSAQSALAAAAAVRDG-APAAYALCRPPGHHARVDAAGGFCYL 190
Query: 168 NNAGLAVQLALNSGCGKVVVIDIDVHYGNGTAEGFYRSNKVLTISLHMNHGSWGPSHPQN 227
NNA +A Q +V V+D D+H+G G E FY VL +S+H + ++ P
Sbjct: 191 NNAAIAAQALRARH-ARVAVLDTDMHHGQGIQEIFYARRDVLYVSIHGDPTNFYP--AVA 247
Query: 228 GTVDELGEGEGFGYNLNIPLPNGTGDRGYVHAMTELVVPAIQKFEPNMIVLVVGQDSSAF 287
G DE G GEG GYN+N+P+P+G+ + + + + + +++F P+ +VL +G D
Sbjct: 248 GFDDERGAGEGLGYNVNLPMPHGSSEAAFFERV-DDALRELRRFAPDALVLSLGFDVYRD 306
Query: 288 DPNGRQCLTMDGYREMGRIVRSLADRYSGGRLLIVQEGGYHVTYSAYCLHATLEGVL 344
DP + +T DG+ +G ++ +L +IVQEGGYH+ + G
Sbjct: 307 DPQSQVAVTTDGFGRLGHLIGALR-----LPTVIVQEGGYHIESLEANARSFFGGFG 358
>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 = 278 bits (713), Expect = 8e-91
Identities = 102/405 (25%), Positives = 175/405 (43%), Gaps = 52/405 (12%)
Query: 4 SPSEPPSPAAEGIINVFWDDGMLNHDTGKGLFDTGFDPGFLEVLEKHPENSDRIKNIVSI 63
S SE P+ + +D ML H G +HPE++ RI++I S
Sbjct: 25 SSSETPARTLPFTTGLIYDSVMLKHQCSCGD------------NSRHPEHAGRIQSIWSR 72
Query: 64 LKRGPISPYISWHSGIPAQIPQLLSFHTPDYINEL------------------------V 99
L+ + G A + +L S H+ ++ V
Sbjct: 73 LQERGLRSQCECLRGRKASLEELQSVHSERHVLLYGTNPLSRLKLDNGKLAGLLAQRMFV 132
Query: 100 EADKAGGKMVCDGTVLNPGSWGAALLAVGTTLSAMKHVLDGHGKIAYALVRPPGHHAQPT 159
G + D S AA A G+ V K +A+VRPPGHHA +
Sbjct: 133 MLPCGGVGVDTDTIWNELHSSNAARWAAGSVTDLAFKVASRELKNGFAVVRPPGHHADHS 192
Query: 160 MADGYCFLNNAGLAVQLALNS-GCGKVVVIDIDVHYGNGTAEGFYRSNKVLTISLH-MNH 217
A G+CF N+ +A + K++++D DVH+GNGT + FY+ VL ISLH +
Sbjct: 193 TAMGFCFFNSVAIACRQLQQQSKASKILIVDWDVHHGNGTQQTFYQDPSVLYISLHRHDD 252
Query: 218 GSWGPSHPQNGTVDELGEGEGFGYNLNIPLPN----GTGDRGYVHAMTELVVPAIQKFEP 273
G++ P +G VDE+G G G G+N+N+ GD Y+ A +V+P ++F P
Sbjct: 253 GNF---FPGSGAVDEVGAGSGEGFNVNVAWAGGLDPPMGDPEYLAAFRIVVMPIAREFSP 309
Query: 274 NMIVLVVGQDSSAFD--PNGRQCLTMDGYREMGRIVRSLADRYSGGRLLIVQEGGYHVTY 331
+++++ G D++ P G ++ + M + + +LA GG +++ EGG+ +T
Sbjct: 310 DLVLVSAGFDAAEGHPAPLGGYHVSAKCFGYMTQQLMNLA----GGAVVLALEGGHDLTA 365
Query: 332 SAYCLHATLEGVLNLPLALLSDPIAYYPEDEAFPVKVIESIKQYQ 376
A + +L + LS+ + ++ +E++ +
Sbjct: 366 ICDASEACVAALLGNRVDPLSEEGWKQKPNLNA-IRSLEAVIRVH 409
>4a69_A Histone deacetylase 3,; transcription, hydrolase; HET: I0P; 2.06A
{Homo sapiens}
Length = 376
Score = 254 bits (650), Expect = 7e-82
Identities = 84/326 (25%), Positives = 135/326 (41%), Gaps = 35/326 (10%)
Query: 19 VFWDDGMLNHDTGKGLFDTGFDPGFLEVLEKHPENSDRIKNIVSILKRGPISPYISWHSG 78
F+D + N G G HP R+ S++ + +
Sbjct: 7 YFYDPDVGNFHYGAG----------------HPMKPHRLALTHSLVLHYGLYKKMIVFKP 50
Query: 79 IPAQIPQLLSFHTPDYINELVEA---------DKAGGKMVCDGTVLNPGSWGAALLAVGT 129
A + FH+ DYI+ L V D + PG + G
Sbjct: 51 YQASQHDMCRFHSEDYIDFLQRVSPTNMQGFTKSLNAFNVGDDCPVFPGLFEFCSRYTGA 110
Query: 130 TLSAMKHVLDGHGKIAYALVRPPGHHAQPTMADGYCFLNNAGLAVQLALNSGCGKVVVID 189
+L + + IA HHA+ A G+C++N+ + + L +V+ ID
Sbjct: 111 SLQGATQLNNKICDIAINW-AGGLHHAKKFEASGFCYVNDIVIGILELLKYHP-RVLYID 168
Query: 190 IDVHYGNGTAEGFYRSNKVLTISLHMNHGSWGPSHPQNGTVDELGEGEGFGYNLNIPLPN 249
ID+H+G+G E FY +++V+T+S H +G++ P G + E+G G Y LN+PL +
Sbjct: 169 IDIHHGDGVQEAFYLTDRVMTVSFHK-YGNY--FFPGTGDMYEVGAESGRYYCLNVPLRD 225
Query: 250 GTGDRGYVHAMTELVVPAIQKFEPNMIVLVVGQDSSAFDPNGRQCLTMDGYREMGRIVRS 309
G D+ Y H ++ + ++P IVL G DS D G L++ G+ E V+S
Sbjct: 226 GIDDQSYKHLFQPVINQVVDFYQPTCIVLQCGADSLGCDRLGCFNLSIRGHGECVEYVKS 285
Query: 310 LADRYSGGRLLIVQEGGYHVTYSAYC 335
LL++ GGY V A C
Sbjct: 286 F-----NIPLLVLGGGGYTVRNVARC 306
>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 = 251 bits (644), Expect = 9e-81
Identities = 86/371 (23%), Positives = 153/371 (41%), Gaps = 47/371 (12%)
Query: 7 EPPSPAAEGIINV---FWDDGMLNHDTGKGLFDTGFDPGFLEVLEKHPENSDRIKNIVSI 63
EP PA G V + ++ + R + S+
Sbjct: 3 EPEEPADSGQSLVPVYIYSPEYVSMCDS------------------LAKIPKRASMVHSL 44
Query: 64 LKRGPISPYISWHSGIPAQIPQLLSFHTPDYINELVEADKAGGKMVCDGTVLN------- 116
++ + + A + ++ +FHT Y+ L + + G D
Sbjct: 45 IEAYALHKQMRIVKPKVASMEEMATFHTDAYLQHLQKVSQEGDDDHPDSIEYGLGYLCPA 104
Query: 117 -PGSWGAALLAVGTTLSAMKHVLDGHGKIAYALVRPPGHHAQPTMADGYCFLNNAGLAVQ 175
G + A G T++A + ++DG K+A HHA+ A G+C+LN+A L +
Sbjct: 105 TEGIFDYAAAIGGATITAAQCLIDGMCKVAINW-SGGWHHAKKDEASGFCYLNDAVLGIL 163
Query: 176 LALNSGCGKVVVIDIDVHYGNGTAEGFYRSNKVLTISLHM-NHGSWGPSHPQNGTVDELG 234
+++ +D+D+H+G+G + F ++KV+T+SLH + G + P G V ++G
Sbjct: 164 RLRR-KFERILYVDLDLHHGDGVEDAFSFTSKVMTVSLHKFSPGFF----PGTGDVSDVG 218
Query: 235 EGEGFGYNLNIPLPNGTGDRGYVHAMTELVVPAIQKFEPNMIVLVVGQDSSAFDPNGRQC 294
G+G Y++N+P+ +G D Y ++ Q F P +VL +G D+ A DP
Sbjct: 219 LGKGRYYSVNVPIQDGIQDEKYYQICESVLKEVYQAFNPKAVVLQLGADTIAGDPMCSFN 278
Query: 295 LTMDGYREMGRIVRSLADRYSGGRLLIVQEGGYHVTYSAYCLHATLEGVLNLPLALLSDP 354
+T G + + + LI+ GGY++ +A C +L LS
Sbjct: 279 MTPVGIGKCLKYILQWQ-----LATLILGGGGYNLANTARCWTYLTGVILGKT---LSSE 330
Query: 355 IAYYPEDEAFP 365
I P+ E F
Sbjct: 331 I---PDHEFFT 338
>3max_A HD2, histone deacetylase 2; class 2, HDAC, foot pocket, hydrolase;
HET: LLX NHE; 2.05A {Homo sapiens}
Length = 367
Score = 251 bits (642), Expect = 1e-80
Identities = 77/340 (22%), Positives = 150/340 (44%), Gaps = 38/340 (11%)
Query: 19 VFWDDGMLNHDTGKGLFDTGFDPGFLEVLEKHPENSDRIKNIVSILKRGPISPYISWHSG 78
++D + N+ G+G HP RI+ ++L + + +
Sbjct: 7 YYYDGDIGNYYYGQG----------------HPMKPHRIRMTHNLLLNYGLYRKMEIYRP 50
Query: 79 IPAQIPQLLSFHTPDYINELVEA---------DKAGGKMVCDGTVLNPGSWGAALLAVGT 129
A ++ +H+ +YI L + V + + G + L+ G
Sbjct: 51 HKATAEEMTKYHSDEYIKFLRSIRPDNMSEYSKQMQRFNVGEDCPVFDGLFEFCQLSTGG 110
Query: 130 TLSAMKHVLDGHGKIAYALVRPPG-HHAQPTMADGYCFLNNAGLAVQLALNSGCGKVVVI 188
+++ + + A+ G HHA+ + A G+C++N+ LA+ L +V+ I
Sbjct: 111 SVAGAVKLN--RQQTDMAVNWAGGLHHAKKSEASGFCYVNDIVLAILELLKYH-QRVLYI 167
Query: 189 DIDVHYGNGTAEGFYRSNKVLTISLHMNHGSWGPSHPQNGTVDELGEGEGFGYNLNIPLP 248
DID+H+G+G E FY +++V+T+S H +G + P G + ++G G+G Y +N P+
Sbjct: 168 DIDIHHGDGVEEAFYTTDRVMTVSFHK-YGEYFPGT---GDLRDIGAGKGKYYAVNFPMR 223
Query: 249 NGTGDRGYVHAMTELVVPAIQKFEPNMIVLVVGQDSSAFDPNGRQCLTMDGYREMGRIVR 308
+G D Y ++ ++ ++P+ +VL G DS + D G LT+ G+ + +V+
Sbjct: 224 DGIDDESYGQIFKPIISKVMEMYQPSAVVLQCGADSLSGDRLGCFNLTVKGHAKCVEVVK 283
Query: 309 SLADRYSGGRLLIVQEGGYHVTYSAYCLHATLEGVLNLPL 348
+ LL++ GGY + A C L+ +
Sbjct: 284 TF-----NLPLLMLGGGGYTIRNVARCWTYETAVALDCEI 318
>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 = 46.2 bits (109), Expect = 1e-05
Identities = 68/452 (15%), Positives = 122/452 (26%), Gaps = 173/452 (38%)
Query: 1 MAASPSEPPSP------AAEG---IINVFWDDGMLNHDTGKGLFDTGFD---------PG 42
MA P + S EG ++ +F G G+G D F+
Sbjct: 132 MAKRPFDKKSNSALFRAVGEGNAQLVAIF---G------GQGNTDDYFEELRDLYQTYHV 182
Query: 43 F-----------LEVLEKHPENSDRIK----NIVSILKRGPISPYISWHSGIPAQIP--- 84
L L + +++++ NI+ L+ +P + IP P
Sbjct: 183 LVGDLIKFSAETLSELIRTTLDAEKVFTQGLNILEWLENPSNTPDKDYLLSIPISCPLIG 242
Query: 85 --QLLSFHTPDYINELVEADKAGGKMVCDGTVLNPGSWGAALLAVGTTLSAMKHVLDGHG 142
QL + +V A G PG + L G T GH
Sbjct: 243 VIQLAHY--------VVTAKLLG---------FTPGELRSYL--KGAT---------GHS 274
Query: 143 KIAYALVRPPGHHAQPTMADGYCFLNNAGLAVQLALNSGCGKVVVIDIDVHYGNGTAEGF 202
+ LV +A+ + E F
Sbjct: 275 Q---GLV--------------------TAVAIAET-------------------DSWESF 292
Query: 203 YR-SNKVLTISLHM---NHGSWGP-SHPQNGTVDELGEGEGF-GYNLNIPLPNGTGDRGY 256
+ K +T+ + + ++ S P + D L EG L+I
Sbjct: 293 FVSVRKAITVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGVPSPMLSI--------SNL 344
Query: 257 VHAMTELVVPAIQKFEPNM----IVLVVGQDSSAFDPNGRQCLTMDGYRE----MGRIVR 308
+ V P I LV NG + L + G + + +R
Sbjct: 345 TQEQVQDYVNKTNSHLPAGKQVEISLV----------NGAKNLVVSGPPQSLYGLNLTLR 394
Query: 309 SLA-----DR----YSGGRLLIVQEGG-----YHVTYSAYCLHATLEGVLNLPLALLSDP 354
D+ +S +L +H S L + + L+ +
Sbjct: 395 KAKAPSGLDQSRIPFSERKLKFSNRFLPVASPFH---SHL-LVPASDLINK---DLVKNN 447
Query: 355 IAYYPEDEAFPVKVIES---IKQYQNDVIPFL 383
+++ +D PV ++ + +
Sbjct: 448 VSFNAKDIQIPVYDTFDGSDLRVLSGSISERI 479
>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 = 37.9 bits (87), Expect = 0.006
Identities = 29/220 (13%), Positives = 60/220 (27%), Gaps = 60/220 (27%)
Query: 187 VIDIDVHYGNGTAEGFYRSNKVLTISLHMNHGSW----------GPSHPQ---NGTVDEL 233
+ + + F L +N+ + PS D L
Sbjct: 67 LFWTLLSKQEEMVQKFVEE------VLRINYK-FLMSPIKTEQRQPSMMTRMYIEQRDRL 119
Query: 234 GEGEGFGYNLNIPLPNGTGDRGYVHAMTELVVPAIQKFEPNMIVLVVGQDSSAFDPNGRQ 293
YN N R + +L A+ + P VL+ G S G+
Sbjct: 120 -------YNDNQVFAKYNVSR--LQPYLKLR-QALLELRPAKNVLIDGVLGS-----GKT 164
Query: 294 CLTMDGYREMGRIVR--------SLADRYSGGRLLIVQEGGYHVTYSAYCLHATLEGVLN 345
+ +D + +L + S +L + + + + + + N
Sbjct: 165 WVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWT--SRSDHSSN 222
Query: 346 LPLALLSDPIAYYPEDEAFPVKVIESIKQYQN------DV 379
+ L + ++ + K Y+N +V
Sbjct: 223 IKLRI---------HSIQAELRRLLKSKPYENCLLVLLNV 253
Score = 32.9 bits (74), Expect = 0.22
Identities = 31/256 (12%), Positives = 64/256 (25%), Gaps = 84/256 (32%)
Query: 181 GCGK-VVVIDIDVHYGNGTAEGFYRSNKVLTISLHMNHG-SW---GPSHPQNGTVDELGE 235
G GK V +D+ S KV M+ W + ++ L
Sbjct: 160 GSGKTWVALDV------------CLSYKVQC---KMDFKIFWLNLKNCNSPETVLEML-- 202
Query: 236 GEGFGYNL------------NIPLPNGTG---------DRGYVHAMTELVV------PAI 268
+ Y + NI L + + Y + + LV+ A
Sbjct: 203 -QKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCL--LVLLNVQNAKAW 259
Query: 269 QKFEPNMIVLVVGQDSSAFD---PNGRQCLTMDGYRE--------------MGRIVRSLA 311
F + +L+ + D +++D + + + L
Sbjct: 260 NAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLP 319
Query: 312 DRYSGGRLLIV-------QEGGYHVTYSAYCLHATLEGVLNLPLALLSDPI--AYY---- 358
+ ++G + L ++ L +L +
Sbjct: 320 REVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLS 379
Query: 359 --PEDEAFPVKVIESI 372
P P ++ I
Sbjct: 380 VFPPSAHIPTILLSLI 395
>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 = 31.5 bits (70), Expect = 0.21
Identities = 9/25 (36%), Positives = 15/25 (60%), Gaps = 3/25 (12%)
Query: 360 EDEAFPVKVIE-SIKQYQNDVIPFL 383
E +A +K ++ S+K Y +D P L
Sbjct: 18 EKQA--LKKLQASLKLYADDSAPAL 40
>3d40_A FOMA protein; fosfomycin, antibiotic resistance, kinase, phosphoryl
transfer, transferase; 1.53A {Streptomyces wedmorensis}
PDB: 3d41_A* 3qun_A* 3quo_A* 3qur_A* 3qvf_A* 3qvh_A*
Length = 286
Score = 31.5 bits (71), Expect = 0.46
Identities = 15/66 (22%), Positives = 24/66 (36%), Gaps = 6/66 (9%)
Query: 258 HAMTELVVPAIQKFEPNMIVLVVGQDSSAF-DPNGRQCLTMDGYREMGRIVRSLADRYSG 316
H + +VP P+ + + VG S F + L D + R R+ A
Sbjct: 8 HHHSSGLVPRGSHMTPDFLAIKVG--GSLFSRKDEPGSLDDD---AVTRFARNFARLAET 62
Query: 317 GRLLIV 322
R +V
Sbjct: 63 YRGRMV 68
>1mhm_A Adometdc, samdc, S-adenosylmethionine decarboxylase; covalent
pyruvoyl group, lyase; 2.30A {Solanum tuberosum} SCOP:
d.156.1.1
Length = 288
Score = 29.6 bits (66), Expect = 1.7
Identities = 9/56 (16%), Positives = 17/56 (30%)
Query: 260 MTELVVPAIQKFEPNMIVLVVGQDSSAFDPNGRQCLTMDGYREMGRIVRSLADRYS 315
+ LV + FEP + + D + + + GY + S
Sbjct: 201 LGPLVERVLACFEPAEFSVALHADVATKLLERICSVDVKGYSLAEWSPEEFGEGGS 256
>1s4n_A Glycolipid 2-alpha-mannosyltransferase; alpha/beta fold,
nucleotide-binding domain, rossmann fold; HET: NAG BMA
MAN NDG; 2.01A {Saccharomyces cerevisiae} SCOP:
c.68.1.16 PDB: 1s4o_A* 1s4p_A*
Length = 348
Score = 29.2 bits (65), Expect = 2.1
Identities = 19/80 (23%), Positives = 30/80 (37%), Gaps = 6/80 (7%)
Query: 27 NHDTGKGLFDTGFDPGFLEVLEKHPENSDRIKNIVSILKRGPISPYISWHSGIPAQIPQL 86
T L+ T ++ ++K+PE D N++S L Y H +I L
Sbjct: 186 YEVTIPTLWQT-----SMDFIKKNPEYLDE-NNLMSFLSNDNGKTYNLCHFWSNFEIANL 239
Query: 87 LSFHTPDYINELVEADKAGG 106
+ +P Y D GG
Sbjct: 240 NLWRSPAYREYFDTLDHQGG 259
>2p4z_A Metal-dependent hydrolases of the beta-lactamase superfamily II;
metal-dependent hydrolases of the beta-lactamase
superfamily hydrolase; 2.10A {Thermoanaerobacter
tengcongensis}
Length = 284
Score = 29.3 bits (65), Expect = 2.2
Identities = 9/37 (24%), Positives = 16/37 (43%)
Query: 25 MLNHDTGKGLFDTGFDPGFLEVLEKHPENSDRIKNIV 61
+L + + DTG F++ + RIK +V
Sbjct: 37 LLKKGNKEIVVDTGQSENFIKNCGLMGIDVGRIKKVV 73
>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 = 28.8 bits (65), Expect = 2.3
Identities = 7/27 (25%), Positives = 13/27 (48%), Gaps = 1/27 (3%)
Query: 170 AGLAVQLALNSGCGKVVVIDIDVHYGN 196
A A L+ V+ +DI + +G+
Sbjct: 23 ANFAFALSQEPD-IHVLAVDISLPFGD 48
>2yib_D RNA-directed RNA polymerase; transferase, reverse transcriptase,
IPNV; 3.80A {Infectious pancreatic necrosis virus}
Length = 770
Score = 29.3 bits (64), Expect = 2.6
Identities = 18/108 (16%), Positives = 40/108 (37%), Gaps = 8/108 (7%)
Query: 39 FDPGFLEVLEKHPENSDRIKNIVSILKRGPISPYISWHSGIPAQIPQLLSFHTPDYINEL 98
P + + + ++ + + +++ G + +S G A P+ FH PD+
Sbjct: 60 LRPRAIPTMVELETDAA-LPRLRQMVEDGKLKDTVSVPEGTTAFYPKYYPFHKPDH---- 114
Query: 99 VEADKAGGKMVCDGTVLNPGSWGAALLAVGTTLSAMKHVLDGHGKIAY 146
D+ G D T+L ++ T ++ V + + Y
Sbjct: 115 ---DEVGTFGAPDITLLKQLTFFLLENDFPTGPETLRQVREAIATLQY 159
>2h5c_A Alpha-lytic protease; serine protease, acylation transition STAT
catalysis, protein folding, protein stability, packing
DIST hydrolase; HET: SO4; 0.82A {Lysobacter enzymogenes}
SCOP: b.47.1.1 PDB: 1p02_A 1p03_A 1p04_A 1p05_A 1p06_A*
1p01_A 1p11_E 1p12_E 1qrx_A* 1tal_A 2alp_A 1ssx_A*
2h5d_A* 2ull_A 3qgj_A* 9lpr_A 1boq_A 1gbj_A 1gbk_A
1gbl_A ...
Length = 198
Score = 28.4 bits (63), Expect = 3.4
Identities = 23/117 (19%), Positives = 34/117 (29%), Gaps = 24/117 (20%)
Query: 118 GSWGAALLAVGTTLSAMKHVLDGHGKIAYALVR-PPGHHAQPTMADGYCFLNNAGLAV-- 174
+ VGT + + D A V P +A+G F+ G
Sbjct: 42 ATARIGGAVVGTFAARVFPGND------RAWVSLTSAQTLLPRVANGSSFVTVRGSTEAA 95
Query: 175 --QLALNSG------CGKVVVIDIDVHYGNGTAEGFYRSNKVLTISLHMNHG-SWGP 222
SG CG + ++ +Y G G + N M G S G
Sbjct: 96 VGAAVCRSGRTTGYQCGTITAKNVTANYAEGAVRGLTQGN------ACMGRGDSGGS 146
>3gkj_A Niemann-PICK C1 protein; oxysterol, cholesterol, cholesterol
transfer, disease mutati endosome, glycoprotein,
lysosome, membrane, transmembrane; HET: NAG HC3; 1.60A
{Homo sapiens} PDB: 3gkh_A* 3gki_A*
Length = 232
Score = 28.1 bits (62), Expect = 4.0
Identities = 7/42 (16%), Positives = 14/42 (33%)
Query: 166 FLNNAGLAVQLALNSGCGKVVVIDIDVHYGNGTAEGFYRSNK 207
FL + + K V ++ + G A Y + +
Sbjct: 100 FLQVTATEDYVDPVTNQTKTNVKELQYYVGQSFANAMYNACR 141
>2pfe_A Protease A, alkaline serine protease, TFPA; beta-barrels,
thermophIle, kinetic stabilit thermostability, protein
folding; HET: 2AB; 1.44A {Thermobifida fusca}
Length = 186
Score = 27.9 bits (62), Expect = 4.7
Identities = 12/42 (28%), Positives = 15/42 (35%), Gaps = 7/42 (16%)
Query: 182 CGKVVVIDIDVHYGNGTAEGFYRSNKVLTISLHMNHG-SWGP 222
CG + + V Y GT G R+ G S GP
Sbjct: 108 CGTIQSKNQTVRYAEGTVTGLTRTTAC------AEGGDSGGP 143
>1gax_A Valrs, valyl-tRNA synthetase; protein-RNA complex, rossmann fold,
coiled coil, riken structural genomics/proteomics
initiative, RSGI; HET: VAA; 2.90A {Thermus thermophilus}
SCOP: a.2.7.3 a.27.1.1 b.51.1.1 c.26.1.1 PDB: 1ivs_A*
1iyw_A
Length = 862
Score = 27.9 bits (63), Expect = 8.0
Identities = 12/79 (15%), Positives = 18/79 (22%), Gaps = 28/79 (35%)
Query: 16 IINVFWDDGMLNHDTGKGLFDTGFD--------------PGFLEVLEKHPEN---SDRIK 58
++V +G + + G D G L E + R
Sbjct: 290 PVSVINLEGRMEGERVPEALR-GLDRFEARRKAVELFREAGHLVKEEDYTIALATCSRCG 348
Query: 59 NIVSILKRGPISPYIS--W 75
PI I W
Sbjct: 349 T--------PIEYAIFPQW 359
>3hut_A Putative branched-chain amino acid ABC transporter; extracellular
ligand-binding receptor,transport protein; 1.93A
{Rhodospirillum rubrum atcc 11170}
Length = 358
Score = 27.2 bits (61), Expect = 9.7
Identities = 7/40 (17%), Positives = 12/40 (30%), Gaps = 2/40 (5%)
Query: 165 CFLNN--AGLAVQLALNSGCGKVVVIDIDVHYGNGTAEGF 202
+ G V VI + +G +A+ F
Sbjct: 120 ITTPAFEGPNNAAWMIGDGFTSVAVIGVTTDWGLSSAQAF 159
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 0.428
Gapped
Lambda K H
0.267 0.0724 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 6,440,344
Number of extensions: 419040
Number of successful extensions: 1152
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1099
Number of HSP's successfully gapped: 46
Length of query: 386
Length of database: 6,701,793
Length adjustment: 95
Effective length of query: 291
Effective length of database: 4,049,298
Effective search space: 1178345718
Effective search space used: 1178345718
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: 58 (26.1 bits)