RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy6001
(327 letters)
>1hd7_A DNA-(apurinic or apyrimidinic site) lyase; DNA repair,
endonuclease, APE1, HAP1, REF-1; 1.95A {Homo sapiens}
SCOP: d.151.1.1 PDB: 1e9n_A 3u8u_A 2isi_A
Length = 318
Score = 330 bits (848), Expect = e-113
Identities = 124/330 (37%), Positives = 179/330 (54%), Gaps = 18/330 (5%)
Query: 2 KRSADVIQKSDDENQIPKKQVKFDISRKKKKMKRSADVIQKSDDENQIPKKQVKFDISHE 61
KR D + + + K + KK K + + P
Sbjct: 3 KRGKKGAVAEDGDELRTEPEAKKSKTAAKKNDKEA---------AGEGPALYEDPPDQKT 53
Query: 62 EGSRKPYTTKVKVSTWNVNGLRACVKKNACVEYILEENPDIMALQQIRCQEDEVPESFRK 121
S KP T +K+ +WNV+GLRA +KK ++++ EE PDI+ LQ+ +C E+++P ++
Sbjct: 54 SPSGKPAT--LKICSWNVDGLRAWIKKKG-LDWVKEEAPDILCLQETKCSENKLPAELQE 110
Query: 122 SLSHYHMFWIGSD--KGQGGVGLLTKEKPLTVKYGIPG-VSNQRGRVITAKFKRFTFITV 178
H +W +G GVGLL+++ PL V YGI +Q GRVI A+F F +T
Sbjct: 111 LPGLSHQYWSAPSDKEGYSGVGLLSRQCPLKVSYGIGDEEHDQEGRVIVAEFDSFVLVTA 170
Query: 179 YVPNSGIKLKAIDFRMIWDQHFYDYIQSELRSNSNIIISGDLNVCLQSIDLANPDKNVKT 238
YVPN+G L +++R WD+ F +++ L S +++ GDLNV + IDL NP N K
Sbjct: 171 YVPNAGRGLVRLEYRQRWDEAFRKFLK-GLASRKPLVLCGDLNVAHEEIDLRNPKGNKKN 229
Query: 239 AGYTVEERRNFRELLD-TGLVDAFRHLYPDEEGAYTYWSFRNKSARLNNKGWRLDYHLVS 297
AG+T +ER+ F ELL L D+FRHLYP+ AYT+W++ AR N GWRLDY L+S
Sbjct: 230 AGFTPQERQGFGELLQAVPLADSFRHLYPNTPYAYTFWTYMMN-ARSKNVGWRLDYFLLS 288
Query: 298 EQLANNIKDCIIRSDVQGSTHCPVVLRLSL 327
L + D IRS GS HCP+ L L+L
Sbjct: 289 HSLLPALCDSKIRSKALGSDHCPITLYLAL 318
>2o3h_A DNA-(apurinic or apyrimidinic site) lyase; APE, endonuclease; 1.90A
{Homo sapiens} PDB: 1bix_A 1dew_A* 1de8_B* 1de9_A*
2o3c_A
Length = 285
Score = 324 bits (832), Expect = e-111
Identities = 113/268 (42%), Positives = 163/268 (60%), Gaps = 7/268 (2%)
Query: 64 SRKPYTTKVKVSTWNVNGLRACVKKNACVEYILEENPDIMALQQIRCQEDEVPESFRKSL 123
S +K+++WNV+GLRA +KK ++++ EE PDI+ LQ+ +C E+++P ++
Sbjct: 21 SPSGKPATLKIASWNVDGLRAWIKKKG-LDWVKEEAPDILCLQETKCSENKLPAELQELP 79
Query: 124 SHYHMFWIGSD--KGQGGVGLLTKEKPLTVKYGIPG-VSNQRGRVITAKFKRFTFITVYV 180
H +W +G GVGLL+++ PL V YGI +Q GRVI A+F F +T YV
Sbjct: 80 GLSHQYWSAPSDKEGYSGVGLLSRQCPLKVSYGIGDEEHDQEGRVIVAEFDSFVLVTAYV 139
Query: 181 PNSGIKLKAIDFRMIWDQHFYDYIQSELRSNSNIIISGDLNVCLQSIDLANPDKNVKTAG 240
PN+G L +++R WD+ F +++ L S +++ GDLNV + IDL NP N K AG
Sbjct: 140 PNAGRGLVRLEYRQRWDEAFRKFLK-GLASRKPLVLCGDLNVAHEEIDLRNPKGNKKNAG 198
Query: 241 YTVEERRNFRELLD-TGLVDAFRHLYPDEEGAYTYWSFRNKSARLNNKGWRLDYHLVSEQ 299
+T +ER+ F ELL L D+FRHLYP+ AYT+W++ AR N GWRLDY L+S
Sbjct: 199 FTPQERQGFGELLQAVPLADSFRHLYPNTPYAYTFWTYMMN-ARSKNVGWRLDYFLLSHS 257
Query: 300 LANNIKDCIIRSDVQGSTHCPVVLRLSL 327
L + D IRS GS HCP+ L L+L
Sbjct: 258 LLPALCDSKIRSKALGSDHCPITLYLAL 285
>3g91_A MTH0212, exodeoxyribonuclease; double-strand specific 3'-5'
exonuclease, AP endonuclease; HET: PG4; 1.23A
{Methanothermobacter thermautotrophicusorganism_taxid}
PDB: 3fzi_A 3g0a_A 3g1k_A 3g2c_A 3g3c_A* 3g3y_A* 3g4t_A*
3g00_A 3g0r_A* 3g2d_A* 3g38_A 3g8v_A* 3ga6_A
Length = 265
Score = 321 bits (824), Expect = e-110
Identities = 92/258 (35%), Positives = 142/258 (55%), Gaps = 8/258 (3%)
Query: 73 KVSTWNVNGLRACVKKNACVEYILEENPDIMALQQIRCQEDEVPESFRKSLSHYHMFWIG 132
K+ +WNVNGLRA +K +++ +EE PDI+ LQ+I+ +++P R + Y F+
Sbjct: 5 KIISWNVNGLRAVHRKGF-LKWFMEEKPDILCLQEIKAAPEQLPRKLR-HVEGYRSFFTP 62
Query: 133 SD-KGQGGVGLLTKEKPLTVKYGIPGVS--NQRGRVITAKFKRFTFITVYVPNSGIKLKA 189
++ KG GV + TK P +++ G GV + GR+ A F F +Y PN + +
Sbjct: 63 AERKGYSGVAMYTKVPPSSLREGF-GVERFDTEGRIQIADFDDFLLYNIYFPNGAMSEER 121
Query: 190 IDFRMIWDQHFYDYIQSELRSNSNIIISGDLNVCLQSIDLANPDKNVKTAGYTVEERRNF 249
+ +++ + F + + E S N+II GD N + IDLA P +N +G+ ER
Sbjct: 122 LKYKLEFYDAFLEDVNRERDSGRNVIICGDFNTAHREIDLARPKENSNVSGFLPVERAWI 181
Query: 250 RELLDTGLVDAFRHLYPDEEGAYTYWSFRNKSARLNNKGWRLDYHLVSEQLANNIKDCII 309
+ ++ G VD FR + G YT+WS+R + AR N GWRLDY V+E+ +K I
Sbjct: 182 DKFIENGYVDTFRMFNS-DPGQYTWWSYRTR-ARERNVGWRLDYFFVNEEFKGKVKRSWI 239
Query: 310 RSDVQGSTHCPVVLRLSL 327
SDV GS HCP+ L + L
Sbjct: 240 LSDVMGSDHCPIGLEIEL 257
>2jc5_A Exodeoxyribonuclease; hydrolase, repair phosphodiesterase, DNA
repair, exonuclease, endonuclease; HET: BCN DIO GOL;
1.50A {Neisseria meningitidis}
Length = 259
Score = 302 bits (777), Expect = e-103
Identities = 78/259 (30%), Positives = 135/259 (52%), Gaps = 9/259 (3%)
Query: 73 KVSTWNVNGLRACVKKNACVEYILEENPDIMALQQIRCQEDEVPESFRKSLSHYHMFWIG 132
K+ + NVNG+R+ KK EYI DI+ +Q+++ QE ++ + + H W
Sbjct: 3 KIISANVNGIRSAYKKGF-YEYIAASGADIVCVQELKAQEADLSADMK-NPHGMHGHWHC 60
Query: 133 SD-KGQGGVGLLTKEKPLTVKYGIPGVS--NQRGRVITAKFKRFTFITVYVPNSGIKLKA 189
++ +G GV + +K KP V+ G+ G+ ++ GR + F R + I++Y+P+ +
Sbjct: 61 AEKRGYSGVAVYSKRKPDNVQIGM-GIEEFDREGRFVRCDFGRLSVISLYLPSGSSAEER 119
Query: 190 IDFRMIWDQHFYDYIQSELRSNSNIIISGDLNVCLQSIDLANPDKNVKTAGYTVEERRNF 249
+ + FY +++ +I++ GD N+ Q+IDL N N K +G+ EER
Sbjct: 120 QQVKYRFLDAFYPMLEAMKNEGRDIVVCGDWNIAHQNIDLKNWKGNQKNSGFLPEEREWI 179
Query: 250 RELLD-TGLVDAFRHLYPDEEGAYTYWSFRNKSARLNNKGWRLDYHLVSEQLANNIKDCI 308
+++ G D +R LYPD G YT+WS R + A + GWR+DY +V+ +LA
Sbjct: 180 GKVIHKLGWTDMWRTLYPDVPG-YTWWSNRGQ-AYAKDVGWRIDYQMVTPELAAKAVSAH 237
Query: 309 IRSDVQGSTHCPVVLRLSL 327
+ D + S H P+V+
Sbjct: 238 VYKDEKFSDHAPLVVEYDY 256
>2j63_A AP-endonuclease; base excision repair, lyase; 2.48A {Leishmania
major}
Length = 467
Score = 273 bits (699), Expect = 5e-89
Identities = 86/381 (22%), Positives = 136/381 (35%), Gaps = 64/381 (16%)
Query: 10 KSDDENQIPKKQVKFDISRKKKKMKRSADVIQKSDDENQIPKKQVKFDISHEEGSRKPYT 69
+ + K + ++ + + + +++
Sbjct: 87 TTGSPARRTSSAAKITNGDAGELIRTAEALAALNAKKSEKEIWSDVVPFVRRTTDSDFDP 146
Query: 70 TKV-KVSTWNVNGLRACVKKNAC--VEYILEENPDIMALQQIRCQEDEVP-ESFRKSLSH 125
+++ K TWNV GLR +KKNA ++ E PD++ LQ+ + DE + +
Sbjct: 147 SRMYKFITWNVAGLRGLLKKNASALRAFMEAEKPDVLCLQETKLNVDEADANATLGVVDG 206
Query: 126 YHMFWIGSD--KGQGGVGLLTKEKPLT------VKYGIPGVSNQR--------------- 162
Y +G G K G S +
Sbjct: 207 YSFVDHPCAFKRGYSGTRTYMKNSTTVKGLHARCTRGFALPSEPQADAAAGSRVLVEGAG 266
Query: 163 ---GRVIT----------AKFKRFTFITVYVPNSGIKLKAIDFRM-IWDQHFYDYIQ--- 205
GRV+T + R + YV NSG+ L + +R+ +D +Y+
Sbjct: 267 DEEGRVLTTFLSPDPDSASSSSRIALVNTYVANSGMGLTRLPYRVQSFDPSMREYLHRLD 326
Query: 206 ---------------SELRSNSNIIISGDLNVCLQSID---LANPDKNVKTAGYTVEERR 247
S I +GDLNV + D + +G+ EER
Sbjct: 327 TWATENAAVPSAAAMGSGSSPHGFIWAGDLNVAERDYDRYYAGTFKSMQECSGFAPEERM 386
Query: 248 NFRELLDT-GLVDAFRHLYPDEEGAYTYWSFRNKSARLNNKGWRLDYHLVSEQLANNIKD 306
+FRE + VD FR LYP Y++WS R R N GWRLDY +VS +LA+ + D
Sbjct: 387 SFRETMQRTNSVDIFRQLYPQAGPVYSFWSQRIN-GRPRNLGWRLDYFVVSSRLASYVVD 445
Query: 307 CIIRSDVQGSTHCPVVLRLSL 327
C V GS HCP + +
Sbjct: 446 CFPMPTVMGSDHCPFQMWMRH 466
>1vyb_A ORF2 contains A reverse transcriptase domain; endonuclease, APE-1
type, retrotransposition, retrotransposon, transferase;
1.8A {Homo sapiens} SCOP: d.151.1.1 PDB: 2v0s_A 2v0r_A
Length = 238
Score = 244 bits (625), Expect = 8e-81
Identities = 50/262 (19%), Positives = 107/262 (40%), Gaps = 34/262 (12%)
Query: 69 TTKVKVSTWNVNGLRACVKKNACVEYILEENPDIMALQQIRCQEDEVPESFRKSLSHYHM 128
+ + + T N+NGL + +K++ +I ++P + +Q+ + + +
Sbjct: 5 NSHITILTLNINGLNSAIKRHRLASWIKSQDPSVCCIQETHLTCRDTHR---LKIKGWRK 61
Query: 129 FWIGSD-KGQGGVGLLTKEKPLTVKYGIPGVSNQRGRVI----TAKFKRFTFITVYVPNS 183
+ + + + GV +L +K I ++ G I + + + T + +Y PN+
Sbjct: 62 IYQANGKQKKAGVAILVSDKTDFKPTKIK--RDKEGHYIMVKGSIQQEELTILNIYAPNT 119
Query: 184 GIKLKAIDFRMIWDQHFYDYIQSELRSNSNIIISGDLNVCLQSIDLANPDKNVKTAGYTV 243
G A F + +S+ +I GD N L ++D + K K
Sbjct: 120 G----APRFIKQVLSDLQRDL------DSHTLIMGDFNTPLSTLDRSTRQKVNK------ 163
Query: 244 EERRNFRELLDTGLVDAFRHLYPDEEGAYTYWSFRNKSARLNNKGWRLDYHLVSEQLANN 303
+ + L L+D +R L+P + YT++S ++ ++D+ + S+ L +
Sbjct: 164 DTQELNSALHQADLIDIYRTLHP-KSTEYTFFSAP------HHTYSKIDHIVGSKALLSK 216
Query: 304 IKDCIIRSDVQGSTHCPVVLRL 325
K I ++ S H + L L
Sbjct: 217 CKRTEIITNY-LSDHSAIKLEL 237
>1ako_A Exonuclease III; AP-endonuclease, DNA repair; 1.70A {Escherichia
coli} SCOP: d.151.1.1
Length = 268
Score = 214 bits (547), Expect = 1e-68
Identities = 78/273 (28%), Positives = 131/273 (47%), Gaps = 28/273 (10%)
Query: 73 KVSTWNVNGLRACVKKNACVEYILEENPDIMALQQIRCQEDEVPESFRKSLSHYHMFWIG 132
K ++N+NGLRA + + + PD++ LQ+ + +D P L Y++F+ G
Sbjct: 2 KFVSFNINGLRARPHQ--LEAIVEKHQPDVIGLQETKVHDDMFPLEEVAKLG-YNVFYHG 58
Query: 133 SDKGQGGVGLLTKEKPLTVKYGIPGV-SNQRGRVITAKFKR----FTFITVYVPN----- 182
KG GV LLTKE P+ V+ G PG + R+I A+ T I Y P
Sbjct: 59 -QKGHYGVALLTKETPIAVRRGFPGDDEEAQRRIIMAEIPSLLGNVTVINGYFPQGESRD 117
Query: 183 SGIKLKAIDFRMIWDQHFYDYIQSELRSNSNIIISGDLNVCLQSIDLANPDKNVKTA--- 239
IK + + Q+ +Y+++EL+ ++ ++I GD+N+ +D+ ++N K
Sbjct: 118 HPIKF---PAKAQFYQNLQNYLETELKRDNPVLIMGDMNISPTDLDIGIGEENRKRWLRT 174
Query: 240 ---GYTVEERRNFRELLDTGLVDAFRHLYPDEEGAYTYWSFRNKSARLNNKGWRLDYHLV 296
+ EER L+ GLVD FRH P ++++ +R+K +N+G R+D L
Sbjct: 175 GKCSFLPEEREWMDRLMSWGLVDTFRHANPQTADRFSWFDYRSK-GFDDNRGLRIDLLLA 233
Query: 297 SEQLANNIKDCIIRSDVQG----STHCPVVLRL 325
S+ LA + I +++ S H PV
Sbjct: 234 SQPLAECCVETGIDYEIRSMEKPSDHAPVWATF 266
>2voa_A AF_EXO, XTHA, exodeoxyribonuclease III; EXOIII, AP endonuclease,
lyase; 1.7A {Archaeoglobus fulgidus}
Length = 257
Score = 203 bits (518), Expect = 3e-64
Identities = 76/264 (28%), Positives = 131/264 (49%), Gaps = 18/264 (6%)
Query: 73 KVSTWNVNGLRACVKKNACVEYILEENPDIMALQQIRCQEDEVPESFRKSLSHYHMFWIG 132
K++T+NVN +R+ + + + ++ E PDI+ +Q+ + + + PE+ + YH+ + G
Sbjct: 3 KIATFNVNSIRS--RLHIVIPWLKENKPDILCMQETKVENRKFPEADFHRIG-YHVVFSG 59
Query: 133 SDKGQGGVGLLTKEKPLTVKYGIPGVSNQRGRVITAKFKRFTFITVYVPNSGIKLKAID- 191
KG+ GV + + E+P V +G+ R+I AK I YVP G ID
Sbjct: 60 -SKGRNGVAIASLEEPEDVSFGLDSEPKDEDRLIRAKIAGIDVINTYVPQ-G---FKIDS 114
Query: 192 ----FRMIWDQHFYDYIQSELRSNSNIIISGDLNVCLQSIDLANPDKNVKTAGYTVEERR 247
+++ W + Y Y+Q + S + GD+NV + ID+ +PDK + + RR
Sbjct: 115 EKYQYKLQWLERLYHYLQKTVDFRSFAVWCGDMNVAPEPIDVHSPDKLKNHVCFHEDARR 174
Query: 248 NFRELLDTGLVDAFRHLYPDEEGAYTYWSFRNKSARLNNKGWRLDYHLVSEQLANNIKDC 307
++++L+ G VD R ++P+ E YT++ +R K A GWR D L + LA DC
Sbjct: 175 AYKKILELGFVDVLRKIHPN-ERIYTFYDYRVKGAIERGLGWRGDAILATPPLAERCVDC 233
Query: 308 IIRSDVQG----STHCPVVLRLSL 327
+ S H P+V +
Sbjct: 234 YADIKPRLAEKPSDHLPLVAVFDV 257
>2jc4_A Exodeoxyribonuclease III; hydrolase, repair phosphodiesterase, DNA
repair, exonuclease, endonuclease; HET: 1PE; 1.90A
{Neisseria meningitidis}
Length = 256
Score = 192 bits (490), Expect = 4e-60
Identities = 70/267 (26%), Positives = 126/267 (47%), Gaps = 28/267 (10%)
Query: 73 KVSTWNVNGLRACVKKNACVEYILEENPDIMALQQIRCQEDEVPESFRKSLSHYHMFWIG 132
K++TWNVN L + + + PDI+ LQ+++ +D+ P + + + +H W G
Sbjct: 2 KITTWNVNSLNV--RLPQVQNLLADNPPDILVLQELKLDQDKFPAAALQMMG-WHCVWSG 58
Query: 133 SDKGQGGVGLLTKEKPLTVKYGIPGVSN--QRGRVITAKFKRFTFITVYVPN-SGI---- 185
K GV ++++ P V +G+P + + QR RVI A I VY N +
Sbjct: 59 -QKTYNGVAIVSRSVPQDVHFGLPALPDDPQR-RVIAATVSGVRVINVYCVNGEALDSPK 116
Query: 186 ---KLKAIDFRMIWDQHFYDYIQSELRSNSNIIISGDLNVCLQSIDLANPDKNVKTAGYT 242
K + W ++++ E+ + +++ GD N+ D +P+K + +
Sbjct: 117 FKYKEQ-------WFAALTEFVRDEMTRHGKLVLLGDFNIAPADADCYDPEKWHEKIHCS 169
Query: 243 VEERRNFRELLDTGLVDAFRHLYPDEEGAYTYWSFRNKSARLNNKGWRLDYHLVSEQLAN 302
ER+ F+ LLD GL D+ R ++P+ YT++ +R + G R+D+ LVS +A
Sbjct: 170 SVERQWFQNLLDLGLTDSLRQVHPE-GAFYTWFDYRGAMFQ-RKLGLRIDHILVSPAMAA 227
Query: 303 NIKDCIIRSDVQG----STHCPVVLRL 325
+KD + + + S H PV
Sbjct: 228 ALKDVRVDLETRALERPSDHAPVTAEF 254
>1wdu_A TRAS1 ORF2P; four-layered alpha/beta sandwich, RNA binding protein;
2.40A {Bombyx mori} SCOP: d.151.1.1
Length = 245
Score = 103 bits (258), Expect = 3e-26
Identities = 33/266 (12%), Positives = 69/266 (25%), Gaps = 36/266 (13%)
Query: 64 SRKPYTTKVKVSTWNVNGLRACVKKNACVEYILEENPDIMALQQIRCQEDEVPESFRKSL 123
R +V N+ + + I +Q+ + + FR
Sbjct: 12 VRPKNGPPYRVLQANLQRKKLATAE--LAIEAATRKAAIALIQEPYVGGAKSMKGFR--- 66
Query: 124 SHYHMFWIGSDK-GQGGVGLLTKEKPLTVKYGIPGVSNQR-GRVITAKFKRFTFITVYVP 181
+F + G + + L V +N I + T ++ Y
Sbjct: 67 -GVRVFQSTAQGDGTVKAAIAVFDHDLDVIQYPQLTTNNIVVVGIRTRAWEITLVSYYFE 125
Query: 182 NSGIKLKAIDFRMIWDQHFYDYIQSELRSNSNIIISGDLNVCLQSIDLANPDKNVKTAGY 241
++ ++ +I GD N
Sbjct: 126 PDKPIESYLEQIKRVERKMGPK---------RLIFGGDANAKSTWWG------------- 163
Query: 242 TVEERRNFRELLDTGLVDAFRHLYPDEEGAYTYWSFRNKSARLNNKGWRLDYHLVSEQLA 301
+ + R G + +E T+ + R + R+D +E +
Sbjct: 164 --SKEDDARGDQLMGTLGELGLHILNEGDVPTFDTIRGGKRYQS----RVDVTFCTEDML 217
Query: 302 NNIKDCIIRSDVQGSTHCPVVLRLSL 327
+ I + D+ S H +V + L
Sbjct: 218 DLIDGWRVDEDLVSSDHNGMVFNIRL 243
>3teb_A Endonuclease/exonuclease/phosphatase; PSI-biology, MCSG, midwest
center for structural genomics; 2.99A {Leptotrichia
buccalis c-1013-b}
Length = 266
Score = 79.1 bits (195), Expect = 3e-17
Identities = 47/291 (16%), Positives = 94/291 (32%), Gaps = 65/291 (22%)
Query: 73 KVSTWNVNGLRAC---VKKNACVEYILEENPDIMALQ-----------QIRCQEDEVPES 118
K+ T NV+ K + I E+ D++A+Q +E+
Sbjct: 5 KILTVNVHAWLEENQMEKIDILARTIAEKQYDVIAMQEVNQLMNNKIIFDDIREENYAWV 64
Query: 119 FRKSLS-----HYHMFW----IGSDKGQGGVGLLTKEKPLTVKY----GIPGVSNQRGR- 164
++L Y++ W IG K GV ++T+ K V R
Sbjct: 65 LLETLQKYTDTDYYLHWSNSHIGFGKYNEGVAVITRHKIKAEDEFYCTFAQSVRTISARR 124
Query: 165 ----VITAKFKRFTFITVYVPNSGIKLKAIDFRMIWDQHFYDYIQSELRSNSNIIISGDL 220
I + + F + ++ L + + I + ++++ I+ GD
Sbjct: 125 IVSITINYEGQDIEFYSCHMN-----LPNCETEDMGKN--IQTILNRTQNSNLKILMGDF 177
Query: 221 NVCLQSIDLANPDKNVKTAGYTVEERRNFRELLDTGLVDAFRHLYPDEEGAYTYWSFRNK 280
N D A Y +L GL D + + ++ T
Sbjct: 178 NT----------DAIGNVAAY--------ENILSQGLFDTYV-MAEKKDDGITVD-KSIH 217
Query: 281 SARLNNKGWRLDYHLVSEQLANNIKDC-IIRSDVQGST---HCPVVLRLSL 327
+ RLDY +++L +K+ +I ++ H + +++
Sbjct: 218 GWDNDKAKKRLDYIFSNKEL--KVKESKVIFNNKNKEIVSDHFGIEVKIEF 266
>3g6s_A Putative endonuclease/exonuclease/phosphatase family protein;
alpha-beta protein, structural genomics, PSI-2; 2.50A
{Bacteroides vulgatus atcc 8482}
Length = 267
Score = 57.7 bits (139), Expect = 9e-10
Identities = 47/288 (16%), Positives = 90/288 (31%), Gaps = 59/288 (20%)
Query: 70 TKVKVSTWNVNGLRACVK----------KNACVEYILEENPDIMALQQI-RCQEDEVPES 118
T V+ +T+N+ R K+ ++I + DI+ +Q++ Q ++
Sbjct: 2 TDVRWATFNI---RYDNPQDSLNNWQYRKDRVCQFIKDHELDIVGMQEVLHNQFQDLRAG 58
Query: 119 FRKSLSHYHMFWIGSDKGQGGVGLLTKEKPLTVKYGI------------PGVSNQRGRVI 166
+ G G+ K+K + G R+
Sbjct: 59 LPEYDGIGVGRDDGKTAGEYAPLFYRKDKYEVLDSNTFWLAENPDSVGMMGWDAVCVRIA 118
Query: 167 T-AKFK-RFTFITVYVPNSGIKLKAIDFRMIWDQHFYDYIQSELRSNSNIIISGDLNVCL 224
T AKFK + T N+ + R I+ E+ +++GD N
Sbjct: 119 TWAKFKDKATGKIFMAVNTHFDHVGEEARRQSALLIIRKIK-EIVGERPAVVTGDFN--- 174
Query: 225 QSIDLANPDKNVKTAGYTVEERRNFRELLDTG--LVDAFRHLYPDEEGAYTYWSFRNKSA 282
+ + + + DA++ YT+ F
Sbjct: 175 -----VTDASDA------------YETITTNEFVMKDAYKTAARVTGVDYTFHDFARIP- 216
Query: 283 RLNNKGWRLDYHLVSEQLANNIKDCIIRSDVQG---STHCPVVLRLSL 327
++D+ V+ Q+ +K C I ++V S H P + L L
Sbjct: 217 --AEDCEKIDFIFVTPQV--LVKSCEIPAEVPEALLSDHNPQLADLEL 260
>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 = 48.9 bits (116), Expect = 1e-06
Identities = 62/353 (17%), Positives = 110/353 (31%), Gaps = 107/353 (30%)
Query: 33 MKRSADVIQK-----SDDENQIPKKQVKFDISH--EEGSRKP---YTTKVKVSTWNVNGL 82
+K SA+ + + D E + +I E S P Y + +S + G+
Sbjct: 188 IKFSAETLSELIRTTLDAEKVFTQG---LNILEWLENPSNTPDKDYLLSIPIS-CPLIGV 243
Query: 83 RACVK-KNACVEYILEENPDIMALQQIR----CQEDEVP----------ESFRKSLSHY- 126
+L P + ++ + V ESF S+
Sbjct: 244 IQLAHYVVTAK--LLGFTPGELR-SYLKGATGHSQGLVTAVAIAETDSWESFFVSVRKAI 300
Query: 127 -HMFWIGSDKGQGGVGLLTKEKPLTVKY------GIP----GVSNQRGRVITAKFKRFTF 175
+F+IG + + P ++ G+P +SN + +
Sbjct: 301 TVLFFIGV-RCYEAYPNTSLP-PSILEDSLENNEGVPSPMLSISNLTQEQVQDYVNKT-- 356
Query: 176 ITVYVPNSGIKLKAIDFRMIWDQHFYDYIQSELRSNS--NIIISGD------LNVCLQSI 227
++P K + I S L N N+++SG LN+ L+
Sbjct: 357 -NSHLPAG----KQV------------EI-S-LV-NGAKNLVVSGPPQSLYGLNLTLRKA 396
Query: 228 DLANPDKNVKTAGYTVEERR-----NFRELLDTG-------LVDAFRHLYPDEEGAYTYW 275
A + ++ ER+ F L LV A + D
Sbjct: 397 K-APSGLDQSRIPFS--ERKLKFSNRF---LPVASPFHSHLLVPASDLINKDLVKN--NV 448
Query: 276 SFRNKSARL---NNKGWRLDYHLVSEQLANNIKDCIIRSDVQ-------GSTH 318
SF K ++ + D ++S ++ I DCIIR V+ +TH
Sbjct: 449 SFNAKDIQIPVYDTFDGS-DLRVLSGSISERIVDCIIRLPVKWETTTQFKATH 500
Score = 41.6 bits (97), Expect = 4e-04
Identities = 46/269 (17%), Positives = 83/269 (30%), Gaps = 108/269 (40%)
Query: 36 SADVIQKSDDENQ-----------IPKKQVKFDISHEEGSRKPYTTKVKVSTWNVNGLRA 84
+++ S + N+ + ++QV+ ++ S P +V++S VNG +
Sbjct: 320 PPSILEDSLENNEGVPSPMLSISNLTQEQVQDYVNKTN-SHLPAGKQVEIS--LVNGAKN 376
Query: 85 CVKKNACVE------YILEENPDIMALQQIRCQED----EVPESFRK-SLSH-------- 125
V V Y L + L++ + +P S RK S+
Sbjct: 377 LV-----VSGPPQSLYGLN-----LTLRKAKAPSGLDQSRIPFSERKLKFSNRFLPVASP 426
Query: 126 YHMFWIGSDKGQGGVGLLTKEKPLTVKYGIPGVSNQRGRVITAK-FKRFTFITVYVPNSG 184
+H S LL L I + AK + I VY G
Sbjct: 427 FH-----SH-------LLVPASDL-----INKDLVKNNVSFNAKDIQ----IPVYDTFDG 465
Query: 185 IKLKAID-------FRMI------WDQ-------HFYDY-------IQSELRSNSN---- 213
L+ + I W+ H D+ + N +
Sbjct: 466 SDLRVLSGSISERIVDCIIRLPVKWETTTQFKATHILDFGPGGASGLGVLTHRNKDGTGV 525
Query: 214 -IIISGDLNVCLQSIDLANPDKNVKTAGY 241
+I++G L++ NPD + G+
Sbjct: 526 RVIVAGTLDI--------NPDDDY---GF 543
Score = 38.5 bits (89), Expect = 0.003
Identities = 31/169 (18%), Positives = 57/169 (33%), Gaps = 63/169 (37%)
Query: 31 KKMKRSADVIQKSDDENQIP--KKQVKFD-----IS---HEEGSR--KPYTTKVKVS--- 75
+K K + + D+++IP ++++KF ++ H S P + +
Sbjct: 394 RKAKAPSGL-----DQSRIPFSERKLKFSNRFLPVASPFH---SHLLVPASDLINKDLVK 445
Query: 76 ---TWNVNGLRACVKKNACVEYILEENPDIMALQQIRCQEDEVPESFRKSLSHYHMFWIG 132
++N ++ V Y + D +R + E + + W
Sbjct: 446 NNVSFNAKDIQIPV-------YDTFDGSD------LRVLSGSISERIVDCIIRLPVKWET 492
Query: 133 S---------DKGQG---GVGLLTKEKPLTVKYGIPGVSNQRG-RVITA 168
+ D G G G+G+LT K G G RVI A
Sbjct: 493 TTQFKATHILDFGPGGASGLGVLTHR----NKDG-------TGVRVIVA 530
Score = 31.9 bits (72), Expect = 0.30
Identities = 17/102 (16%), Positives = 36/102 (35%), Gaps = 24/102 (23%)
Query: 192 FRMIW---DQHFYDYIQSELRSNSNIIISGDLNVCLQSIDLANP-DKNVKTAGYTVEE-R 246
+ +W D HF D + I + NP + + G + R
Sbjct: 1642 AQDVWNRADNHFKD----------------TYGFSILDIVINNPVNLTIHFGGEKGKRIR 1685
Query: 247 RNFRELLDTGLVDA---FRHLYPDEEGAYTYWSFRNKSARLN 285
N+ ++ +VD ++ + T ++FR++ L+
Sbjct: 1686 ENYSAMIFETIVDGKLKTEKIFKEINEHSTSYTFRSEKGLLS 1727
Score = 31.9 bits (72), Expect = 0.31
Identities = 44/270 (16%), Positives = 82/270 (30%), Gaps = 97/270 (35%)
Query: 8 IQKSDDENQIPK-KQVKFDISRKKK-KMKRSADVIQKSDDENQIPKKQVK--------FD 57
I N P + F + K+ + SA + + D +K K +
Sbjct: 1661 ILDIVINN--PVNLTIHFGGEKGKRIRENYSAMIFETIVDGKLKTEKIFKEINEHSTSYT 1718
Query: 58 ISHEEG--SRKPYT----TKVKVSTWNVNGLRA--CVKKNACV------EY--------I 95
E+G S +T T ++ + + L++ + +A EY +
Sbjct: 1719 FRSEKGLLSATQFTQPALTLMEKAAFED--LKSKGLIPADATFAGHSLGEYAALASLADV 1776
Query: 96 LE-ENPDIMALQQIR--CQEDEVPESFRKSLSHYHMFWIGSDKGQGGVGLLTKEKPLTVK 152
+ E ++ + R + VP S+Y M I + G+ ++E ++
Sbjct: 1777 MSIE--SLVEVVFYRGMTMQVAVPRD-ELGRSNYGM--IAINPGRVAASF-SQE---ALQ 1827
Query: 153 YGIPGVSNQRGRVITAKFKRFTFITV-YVPNSGIKLKAIDFRMIWDQHFYDYIQSELRSN 211
Y + V + G ++ V Y N N
Sbjct: 1828 YVVERVGKRTGWLVEI---------VNY--NV--------------------------EN 1850
Query: 212 SNIIISGD----------LNVC-LQSIDLA 230
+ +GD LN LQ ID+
Sbjct: 1851 QQYVAAGDLRALDTVTNVLNFIKLQKIDII 1880
>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 = 42.9 bits (100), Expect = 1e-04
Identities = 42/274 (15%), Positives = 81/274 (29%), Gaps = 70/274 (25%)
Query: 87 KKNACVEYILEENPDIMALQQIRCQEDEVPESFRKSLSHYHMFWIGSDKGQGGVGLLTKE 146
N + + + I++ ++I D + S +FW K + V +E
Sbjct: 30 VDNFDCKDVQDMPKSILSKEEI----DHIIMSKDAVSGTLRLFWTLLSKQEEMVQKFVEE 85
Query: 147 KPLTVKYG-----IPGVSNQRGRV----ITAKFKRFTFITVYVPNSGIKLKAIDFRMIWD 197
L + Y I Q + I + + + V+ +
Sbjct: 86 V-LRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAK-----------YNVSR 133
Query: 198 QHFYDYIQS---ELRSNSNIIISGD---------LNVCL-QSIDLANPDK-------NVK 237
Y ++ ELR N++I G L+VCL + K N
Sbjct: 134 LQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCN 193
Query: 238 TAGYTVEERRNFRELLDTGLVDAFRHLYPDEEGAYTYWSFRNKSARLNNKGWRLDYHLVS 297
+ +E + +D H + R+++ L L S
Sbjct: 194 SPETVLEMLQKLLYQIDPNWTSRSDHSSNIKL-------------RIHSIQAELRRLLKS 240
Query: 298 EQLANNIKDC-IIRSDVQGSTH-------CPVVL 323
+ N C ++ +VQ + C ++L
Sbjct: 241 KPYEN----CLLVLLNVQNAKAWNAFNLSCKILL 270
Score = 41.4 bits (96), Expect = 4e-04
Identities = 42/324 (12%), Positives = 104/324 (32%), Gaps = 76/324 (23%)
Query: 6 DVIQKSDDENQIPKK--QVKFDISR--KKKKMKRSADVIQKSDD-ENQIPKKQVK-FDIS 59
+ +SD + I + ++ ++ R K K + V+ + +N K F++
Sbjct: 212 NWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVL---LNVQN---AKAWNAFNL- 264
Query: 60 HEEGSRKPYTTKVKVSTWNVNGLRACVKKNACVEYIL-----EENPDIMALQQIRCQEDE 114
+ TT+ K T + L A + +++ +E ++ + + C+ +
Sbjct: 265 ---SCKILLTTRFKQVT---DFLSAATTTHISLDHHSMTLTPDEVKSLLL-KYLDCRPQD 317
Query: 115 VPESFRKSLSHYHMFWIGSDKGQGGVGLLTKEKPLTVKYGIPGVSNQRGRVITAKF---- 170
+P + + + + ++ T ++ +I +
Sbjct: 318 LPREVLTT----NPRRLS------IIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLE 367
Query: 171 -----KRFTFITVYVPNSGIKLKAIDFRMIWDQHFYD---YIQSELRSNSNIIISGDLNV 222
K F ++V+ P++ I + +IW + ++L S ++
Sbjct: 368 PAEYRKMFDRLSVFPPSAHIPTILLS--LIWFDVIKSDVMVVVNKLHKYS--LVEKQPKE 423
Query: 223 CLQSI-----DLANPDKNVKTAGYTVEERRNFRELLDTGLVDAFRHLYPDEEGAYTYWSF 277
SI +L +N ++ + N + D+ L P Y Y
Sbjct: 424 STISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSD------DLIPPYLDQYFYS-- 475
Query: 278 RNKSARLNNKGWRLDYHLVSEQLA 301
+ +HL + +
Sbjct: 476 ------------HIGHHLKNIEHP 487
Score = 31.7 bits (71), Expect = 0.36
Identities = 35/268 (13%), Positives = 69/268 (25%), Gaps = 110/268 (41%)
Query: 95 ILEENPDIMA--LQQIRCQ-EDEVPESFRKSLSHYHMFWIGSDKGQGGVGLLTKEKPLTV 151
+ + I L I L Y L +++P
Sbjct: 380 VFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKY---------------SLVEKQPKES 424
Query: 152 KYGIPGV--------SNQRG---RVITAKFKRFTFITVYVPNSGIKLKAIDFRMIWDQHF 200
IP + N+ ++ + + + I DQ+F
Sbjct: 425 TISIPSIYLELKVKLENEYALHRSIVD----HYNIPKTFDSDDLIPPY-------LDQYF 473
Query: 201 YDYIQSELRSNSNIIISGDLNVCLQSIDLANPDKNVKTAGYTVEERRNFRELLDTGLVDA 260
Y +I G+ + + + +
Sbjct: 474 YSHI-----------------------------------GH------HLKNIEHPERMTL 492
Query: 261 FRHLYPDEEGAYTYWSF-----RNKSARLNNKGWRLD-------Y-------HLVSEQLA 301
FR ++ D + F R+ S N G L+ Y E+L
Sbjct: 493 FRMVFLD-------FRFLEQKIRHDSTAWNASGSILNTLQQLKFYKPYICDNDPKYERLV 545
Query: 302 NNIKDCIIR--SDVQGSTHCPVVLRLSL 327
N I D + + ++ S + ++ R++L
Sbjct: 546 NAILDFLPKIEENLICSKYTDLL-RIAL 572
>2ddr_A Sphingomyelin phosphodiesterase; DNAse I like folding, riken
structural genomics/proteomics initiative, RSGI,
structural genomics, hydrolase; 1.40A {Bacillus cereus}
SCOP: d.151.1.3 PDB: 2dds_A 2ddt_A* 2uyr_X
Length = 306
Score = 41.6 bits (97), Expect = 2e-04
Identities = 52/321 (16%), Positives = 89/321 (27%), Gaps = 80/321 (24%)
Query: 67 PYTTKVKVSTWNVNGLRACVKKN--------ACVEYILEENPDIMALQQIRCQED----- 113
+KV T NV L + N +N D++ L ++
Sbjct: 5 TQNDTLKVMTHNVYMLSTNLYPNWGQTERADLIGAADYIKNQDVVILNEVFDNSASDRLL 64
Query: 114 ------------EVPESFRKSLSHYHMFWIGSDKGQGGVGLLTK-------EKPLTVKYG 154
+ S + S GGV +++K + G
Sbjct: 65 GNLKKEYPNQTAVLGRSSGSEWDKTLGNYSSSTPEDGGVAIVSKWPIAEKIQYVFAKGCG 124
Query: 155 IPGVSNQRGRVITAKFKRFTFITVYV------PNSGIKLKAIDFRMIWDQHFYDYIQSEL 208
+SN +G V T K F+ V + K R + D+I+++
Sbjct: 125 PDNLSN-KGFVYTKIKKNDRFVHVIGTHLQAEDSMCGKTSPASVRTNQLKEIQDFIKNKN 183
Query: 209 RSNSN-IIISGDLNVCLQSIDLANPDKNVKTAGYTVEERRNFRELLDTGLVDAFRHLYPD 267
N+ ++I GD+NV + + N + + P
Sbjct: 184 IPNNEYVLIGGDMNVNKINAENNNDSEY-------------------ASMFKTLNASVPS 224
Query: 268 EEG-AYTYWSFRNKSARLNNKGW---RLDY------HLVSEQLANNIKDCIIRSDVQGST 317
G T+ + N A+ N LDY H + N + S
Sbjct: 225 YTGHTATWDATTNSIAKYNFPDSPAEYLDYIIASKDHANPSYIENKVLQPKSPQWTVTSW 284
Query: 318 -----------HCPVVLRLSL 327
H PV +S+
Sbjct: 285 FQKYTYNDYSDHYPVEATISM 305
>3l1w_A Uncharacterized protein; APC29019.2, conserved protein,
enterococcus faecalis V583, PSI-2, MCSG, structural
genomics; 1.60A {Enterococcus faecalis}
Length = 257
Score = 40.4 bits (94), Expect = 4e-04
Identities = 39/275 (14%), Positives = 84/275 (30%), Gaps = 43/275 (15%)
Query: 72 VKVSTWNVNGLRACVK----------KNACVEYILEENPDIMALQQIR-CQEDEVPESFR 120
+K++T+NV R + K A + I + + +Q++R Q ++
Sbjct: 1 MKIATYNV---RVDTEYDQDWQWSFRKEAVCQLINFHDWSLCCIQEVRPNQVRDLKA--Y 55
Query: 121 KSLSHYHMFWIGSDKGQGGVGLLTKEKPLTVKYG---IPGVSNQRGRVITAKFKRF-TFI 176
+ + G +G+G L ++K + G + Q A R +
Sbjct: 56 TTFTCLSAEREGDGQGEGLAILYNEQKVQAIDTGYFWLSETPQQPSIHPEAGCPRIALWG 115
Query: 177 TVYVPNSGIKLKAIDFRMIWDQHFYDYIQSELRSNSNIIISGDLNVCLQSIDLANPDKNV 236
++ + H D+I + R +I L+ +
Sbjct: 116 LFKETTQNTP------FLVINVHL-DHISAHARLAGMTVI-------LEELHDKIAQYPT 161
Query: 237 KTAG-YTVEERRNFRELLDTGLVDAFRHLYPDEEGAYTYWSFRNKSARLNNKGWRLDYHL 295
G + E +L+ D+ +L T+ +F + + +DY
Sbjct: 162 LLMGDFNAESGEEVHQLVQKKFQDSK-NLATHYGPRGTFQNF--TYTKPWAELEEIDYIY 218
Query: 296 VSEQLANNIKDCIIRSDVQGST---HCPVVLRLSL 327
V + + G H P+ ++
Sbjct: 219 VKGWQVQQTA--SLTDSIDGRFPSDHFPLEAEVAG 251
>3mpr_A Putative endonuclease/exonuclease/phosphatase FAM protein;
structural genomics, PSI-2, protein structure
initiative; HET: MSE PEG; 1.90A {Bacteroides
thetaiotaomicron}
Length = 298
Score = 40.5 bits (94), Expect = 5e-04
Identities = 36/263 (13%), Positives = 74/263 (28%), Gaps = 63/263 (23%)
Query: 70 TKVKVSTWNV---------NGLRACVKKNACVEYILEENPDIMALQQIRCQEDEVPES-- 118
T + V+++N+ G + + + + DI Q E
Sbjct: 5 TSLTVASYNLRNANGSDSARGDGWGQRYPVIAQMVQYHDFDIFGTQ-------ECFLHQL 57
Query: 119 --FRKSLSHYHMFWIGSDKGQG---GVGLLTKEKPLT-VKYGIPGVS---NQRGRVITAK 169
+++L Y +G D G+ + + V+ G +S + + A
Sbjct: 58 KDMKEALPGYDYIGVGRDDGKDKGEHSAIFYRTDKFDIVEKGDFWLSETPDVPSKGWDAV 117
Query: 170 FKRF-TFITVYVPNSGIKLKAIDFRMIWDQHFYDYIQSEL----------RSNSNIIISG 218
R ++ ++G + + M + L N I++G
Sbjct: 118 LPRICSWGHFKCKDTGFEFLFFNLHMDHIGKKARVESAFLVQEKMKELGRGKNLPAILTG 177
Query: 219 DLNVCLQSIDLANPDKNVKTAGYTVEERRNFRELLDTG-LVDAFRHLYPDEEGAYTYWSF 277
D N + + + G L D++ T+ +F
Sbjct: 178 DFN--------VDQTHQS------------YDAFVSKGVLCDSYEKCDYRYALNGTFNNF 217
Query: 278 RNKSARLNNKGWRLDYHLVSEQL 300
S R+D+ VS
Sbjct: 218 DPNS----FTESRIDHIFVSPSF 236
>2ei9_A Non-LTR retrotransposon R1BMKS ORF2 protein; four layered alpha
beta sandwich, gene regulation; 2.00A {Bombyx mori}
Length = 240
Score = 39.2 bits (90), Expect = 0.001
Identities = 25/258 (9%), Positives = 71/258 (27%), Gaps = 46/258 (17%)
Query: 71 KVKVSTWNVNGLRACVKKNACVEYILEENPDIMALQQIRCQEDEVPESFRKSLSHYHMFW 130
++++ N+ G + DI+ +Q+ + + +
Sbjct: 7 RLRIGQINLGGAED--ATRELPSIARDLGLDIVLVQE----------------QYSMVGF 48
Query: 131 IGSDKGQGGVGLLTKEKPLTVKYGIPGVSNQRGRVITAKFKRFTFITVYVPNSGIKLKAI 190
+ G+ + + L + +S+ V+ ++ Y S +
Sbjct: 49 LAQCGAHPKAGVYIRNRVLPC-AVLHHLSSTHITVVHIGGWDLYMVSAYFQYSDPIDPYL 107
Query: 191 DFRMIWDQHFYDYIQSELRSNSNIIISGDLNVCLQSIDLANPDKNVKTAGYTVEERRNFR 250
+ ++I D N ++ + R
Sbjct: 108 HRLGNILDRL---------RGARVVICADTNAHSPL------WHSLPRHYVGRGQEVADR 152
Query: 251 ELLDTGLVDAFRHLYPDEEG-AYTYWSFRNKSARLNNKGWRLDYHLVSEQLANNIKDCII 309
+ A R + + +G T+ + +S +D L + + + + +
Sbjct: 153 RAKMEDFIGARRLVVHNADGHLPTFSTANGES--------YVDVTLSTRGVR--VSEWRV 202
Query: 310 RSDVQGSTHCPVVLRLSL 327
++ S H +V +
Sbjct: 203 TNES-SSDHRLIVFGVGG 219
>3i41_A Beta-hemolysin; beta toxin, sphingomyelinase, toxin; 1.75A
{Staphylococcus aureus} PDB: 3i46_A 3i48_A 3i5v_A*
3k55_A
Length = 317
Score = 37.8 bits (87), Expect = 0.003
Identities = 38/276 (13%), Positives = 77/276 (27%), Gaps = 68/276 (24%)
Query: 64 SRKPYTTKVKVSTWNVNGLRACVKKN--------ACVEYILEENPDIMALQQIRCQED-- 113
K T +K+ + NV L + N + +N D++ +
Sbjct: 22 ESKKDDTDLKLVSHNVYMLSTVLYPNWGQYKRADLIGQSSYIKNNDVVIFNEAFDNGASD 81
Query: 114 --------------EVPESFRKSLSHYHMFWIGSDKGQGGVGLLTK-----EKPLTVKYG 154
V + + + GGV +++K + K G
Sbjct: 82 KLLSNVKKEYPYQTPVLGRSQSGWDKTEGSYSSTVAEDGGVAIVSKYPIKEKIQHVFKSG 141
Query: 155 IPGVSNQRGRVITAKF----KRFTFITV-----YVPNSGIKLKAIDFRMIWDQHFYDYIQ 205
++ + K K I + I + + D+++
Sbjct: 142 CGFDNDSNKGFVYTKIEKNGKNVHVIGTHTQSEDSRCGAGHDRKIRAEQMKE--ISDFVK 199
Query: 206 SE-LRSNSNIIISGDLNVCLQSIDLANPDKNVKTAGYTVEERRNFRELLDTGLVDAFRHL 264
+ + + + I GDLNV + + F+++L V+ +
Sbjct: 200 KKNIPKDETVYIGGDLNVNKGTPE--------------------FKDMLKNLNVNDVLYA 239
Query: 265 YPDEEGAYTYWSFRNKSARLNN---KGWRLDYHLVS 297
+ T+ N A+ N K LDY
Sbjct: 240 GHN----STWDPQSNSIAKYNYPNGKPEHLDYIFTD 271
>1zwx_A SMCL, sphingomyelinase-C; dnase1-like fold, beta-hairpin,
hydrolase; 1.90A {Listeria ivanovii} SCOP: d.151.1.3
Length = 301
Score = 36.2 bits (83), Expect = 0.009
Identities = 38/274 (13%), Positives = 70/274 (25%), Gaps = 69/274 (25%)
Query: 67 PYTTKVKVSTWNVNGLRACVKKN--------ACVEYILEENPDIMALQQIRCQEDEVPES 118
Y K+++ NV + N + +N D++ L +
Sbjct: 6 EYPGNFKITSHNVYLFSRNIYPNWGQMHRADLIAQADYMKNNDVVILNEAFDTSAS--HR 63
Query: 119 FRKSLSHYH------------------MFWIGSDKGQGGVGLLTK-------EKPLTVKY 153
+L + + GGV ++++ +
Sbjct: 64 LLNNLREMYPHQTPVIGRSKHGWDKTEGNYSNFALEDGGVAVVSQWPIVEKSQHIFQRGG 123
Query: 154 GIPGVSNQRGRVITAKFKRFTFITVYV------PNSGIKLKAIDFRMIWDQHFYDYIQSE 207
G +SN +G K + + K + R Q +I +
Sbjct: 124 GADRLSN-KGFAYVKIMKNGKPYHIIGTHTQADDSLISKDTSRAIRAEQMQEIQTFIAKK 182
Query: 208 LRSNSN-IIISGDLNVCLQSIDLANPDKNVKTAGYTVEERRNFRELLDTGLVDAFRHLYP 266
I I GDLNV + +E + +LL+ +
Sbjct: 183 NIPKDEIIFIGGDLNVNYGT-----------------DEYHDMLKLLN--VSSPANFNGQ 223
Query: 267 DEEGAYTYWSFRN---KSARLNNKGWRLDYHLVS 297
T+ N K + LDY V
Sbjct: 224 ----MATWDPTTNSMLKESYPKAAPEYLDYIFVE 253
>2a40_B Deoxyribonuclease-1; WAVE, WH2, WAsp, actin, DNAse I, ARP2/3,
structural protein; HET: HIC NAG ATP; 1.80A {Bos taurus}
SCOP: d.151.1.1 PDB: 1dnk_A* 2a3z_B* 2a41_B* 2a42_B*
2d1k_B* 2dnj_A* 3cjc_D* 3dni_A* 1atn_D*
Length = 260
Score = 32.0 bits (72), Expect = 0.22
Identities = 40/290 (13%), Positives = 83/290 (28%), Gaps = 65/290 (22%)
Query: 72 VKVSTWNVNGL-RACVKKNACVEYILE--ENPDIMALQQIRCQEDEVPESFRKSL----- 123
+K++ +N+ + YI+ DI+ +Q++R L
Sbjct: 1 LKIAAFNIRTFGETKMSNATLASYIVRIVRRYDIVLIQEVRDSHLVAVGKLLDYLNQDDP 60
Query: 124 SHYHMFW---IGSDKGQGGVGLLTKEKPLTVK-------YGIPGVSNQRGR---VITAKF 170
+ YH +G + + L + ++V ++ R V+
Sbjct: 61 NTYHYVVSEPLGRNSYKERYLFLFRPNKVSVLDTYQYDDGCESCGNDSFSREPAVVKFSS 120
Query: 171 KRFTFITVYVPNSGIKLKAIDFRMIWDQHFYDYIQSELRSNSNIIISGDLNVCLQSIDLA 230
+ + Y +Q + +++++ GD
Sbjct: 121 HSTKVKEFAIVALHSAPSDAVAEINSLYDVYLDVQQKWH-LNDVMLMGDF---------- 169
Query: 231 NPDKNVKTAGYTVEERRNFRELLDTGLVDAFRHLYPDEEGAYTYWSFRNKSARLNNKGWR 290
N + T + + R + F+ L PD A T + N +
Sbjct: 170 ----NADCSYVTSSQWSSIRLRTSST----FQWLIPDS--ADTTATSTNCA--------- 210
Query: 291 LDYHLVSEQLANN--IKDCIIRSDVQG------------STHCPVVLRLS 326
D +V+ L + + D Q S H PV + L+
Sbjct: 211 YDRIVVAGSLLQSSVVPGSAAPFDFQAAYGLSNEMALAISDHYPVEVTLT 260
>3mtc_A Type II inositol-1,4,5-trisphosphate 5-phosphatas;
INPP5BA,phosphoinositide 5-phosphatase, inositol
signalling, phosphatase, magnesium; HET: PIF; 2.40A
{Homo sapiens} PDB: 3n9v_A
Length = 313
Score = 30.5 bits (69), Expect = 0.76
Identities = 15/68 (22%), Positives = 22/68 (32%), Gaps = 9/68 (13%)
Query: 68 YTT----KVKVSTWNVNGLRACVKKNACVEYILEENPDIMALQQIRCQE-DEVPESFRKS 122
YT + T+NVNG C+ L + + QE D E+F
Sbjct: 2 YTYIQNFRFFAGTYNVNG----QSPKECLRLWLSNGIQAPDVYCVGFQELDLSKEAFFFH 57
Query: 123 LSHYHMFW 130
+ W
Sbjct: 58 DTPKEEEW 65
>3oll_A Estrogen receptor beta; steroid binding, phosphorylation, hormone
receptor-activator; HET: PTR EST; 1.50A {Homo sapiens}
PDB: 1u3s_A* 1u3q_A* 1x78_A* 1x7b_A* 1x7j_A* 1x76_A*
2yjd_A* 3ols_A* 3omo_A* 3omp_A* 3omq_A* 1u3r_A* 1u9e_A*
1qkm_A* 2giu_A* 1nde_A* 2jj3_A* 2i0g_A* 2qtu_A* 2z4b_A*
...
Length = 240
Score = 30.1 bits (68), Expect = 0.88
Identities = 18/81 (22%), Positives = 33/81 (40%), Gaps = 8/81 (9%)
Query: 222 VCLQSIDLANPD-KNVKTAGYTVEERRNFRELLDTGLVDAFRHLYPDEEGAYTYWSFRNK 280
+C++++ L N + TA + R LL+ + DA + A + S + +
Sbjct: 138 LCVKAMILLNSSMYPLVTATQDADSSRKLAHLLNA-VTDALVWV-----IAKSGISSQQQ 191
Query: 281 SARLNNKGWRLDY-HLVSEQL 300
S RL N L + S +
Sbjct: 192 SMRLANLLMLLSHVRHASNKG 212
>3ngq_A CCR4-NOT transcription complex subunit 6-like; alpha/beta sandwich
fold, hydrolase; HET: 1PS; 1.80A {Homo sapiens} PDB:
3ngo_A 3ngn_A
Length = 398
Score = 29.2 bits (64), Expect = 2.2
Identities = 17/95 (17%), Positives = 33/95 (34%), Gaps = 18/95 (18%)
Query: 58 ISHEEGSRKPYTTKVKVSTWNV----------------NGLRACVKKNACVEYILEENPD 101
I+ +E + + V +NV L +K +E I+ + D
Sbjct: 18 ITLKERDQILPSASFTVMCYNVLCDKYATRQLYGYCPSWALNWEYRKKGIMEEIVNCDAD 77
Query: 102 IMALQQIRCQEDEVPESFRKSLSHYHMFWIGSDKG 136
I++LQ+ + ++ F +L S K
Sbjct: 78 IISLQE--VETEQYFTLFLPALKERGYDGFFSPKS 110
>4a9c_A Phosphatidylinositol-3,4,5-trisphosphate 5-phosph; SGC, signalling,
structural genomics consortium stockholm, magnesium
binding, hydrolase; HET: B5F; 2.10A {Homo sapiens} PDB:
3nr8_B*
Length = 316
Score = 28.7 bits (64), Expect = 2.3
Identities = 29/187 (15%), Positives = 49/187 (26%), Gaps = 38/187 (20%)
Query: 71 KVKVSTWNVNG----------LRACVKKNACVEYILEENPDIMAL--QQIRCQEDEVPES 118
V + TWN+ + E + DI Q+ + E +
Sbjct: 9 SVFIGTWNMGSVPPPKNVTSWFTSKGLGKTLDEVTVTIPHDIYVFGTQENSVGDREWLDL 68
Query: 119 FRKSLSHYHMFW---IGSDKGQGGVGLL-----------TKEKPLTVKYGIPGVSNQRGR 164
R L I + + + + +VK GI +G
Sbjct: 69 LRGGLKELTDLDYRPIAM-QSLWNIKVAVLVKPEHENRISHVSTSSVKTGIANTLGNKGA 127
Query: 165 VITAKFK----RFTFITVYVP--NSGIKLKAIDFRMIWDQHFYDYIQSELRSNSN----I 214
V F F F+ ++ N + ++ I Q S +
Sbjct: 128 VGV-SFMFNGTSFGFVNCHLTSGNEKTARRNQNYLDILRLLSLGDRQLNAFDISLRFTHL 186
Query: 215 IISGDLN 221
GDLN
Sbjct: 187 FWFGDLN 193
>1yye_A ER-beta, estrogen receptor beta; ER-beta, nuclear receptor,
transcription factor, agonist; HET: 196; 2.03A {Homo
sapiens} SCOP: a.123.1.1 PDB: 1yy4_A*
Length = 268
Score = 28.3 bits (63), Expect = 3.0
Identities = 18/81 (22%), Positives = 33/81 (40%), Gaps = 8/81 (9%)
Query: 222 VCLQSIDLANPD-KNVKTAGYTVEERRNFRELLDTGLVDAFRHLYPDEEGAYTYWSFRNK 280
+C++++ L N + TA + R LL+ + DA + A + S + +
Sbjct: 136 LCVKAMILLNSSMYPLVTATQDADSSRKLAHLLNA-VTDALVWV-----IAKSGISSQQQ 189
Query: 281 SARLNNKGWRLDY-HLVSEQL 300
S RL N L + S +
Sbjct: 190 SMRLANLLMLLSHVRHASNKG 210
>3ecq_A Protein SPR0328, endo-alpha-N-acetylgalactosaminidase; distorted
(beta/alpha)8 (TIM) barrel glycoside hydrolase DOM WALL;
2.90A {Streptococcus pneumoniae}
Length = 1531
Score = 28.7 bits (63), Expect = 3.1
Identities = 10/48 (20%), Positives = 20/48 (41%), Gaps = 3/48 (6%)
Query: 244 EERRNFRELLDTGLVDAFRHLYPDEEGAYTYWSFRNKSARLNNKGWRL 291
+ ++ + LD VD + + G W+ + +N +GWR
Sbjct: 713 DLKKKLGDGLDFIYVDVW---GNGQSGDNGAWATHVLAKEINKQGWRF 757
>1l2j_A Estrogen receptor beta; nuclear receptor, transcription factor,
antagonist transcription receptor; HET: ETC; 2.95A {Homo
sapiens} SCOP: a.123.1.1
Length = 271
Score = 28.4 bits (63), Expect = 3.3
Identities = 18/81 (22%), Positives = 33/81 (40%), Gaps = 8/81 (9%)
Query: 222 VCLQSIDLANPD-KNVKTAGYTVEERRNFRELLDTGLVDAFRHLYPDEEGAYTYWSFRNK 280
+C++++ L N + TA + R LL+ + DA + A + S + +
Sbjct: 164 LCVKAMILLNSSMYPLVTATQDADSSRKLAHLLNA-VTDALVWV-----IAKSGISSQQQ 217
Query: 281 SARLNNKGWRLDY-HLVSEQL 300
S RL N L + S +
Sbjct: 218 SMRLANLLMLLSHVRHASNKG 238
>2ww8_A RRGA, cell WALL surface anchor family protein; IGG, pilus, CNA_B,
adhesin, integrin, cell adhesion; HET: EPE; 1.90A
{Streptococcus pneumoniae}
Length = 893
Score = 28.6 bits (61), Expect = 4.0
Identities = 13/84 (15%), Positives = 22/84 (26%), Gaps = 6/84 (7%)
Query: 15 NQIPKKQVKFDISRKKKKMKRSADVIQKSDDENQIPKKQVKFDISHEEGSRKPYTTKVKV 74
+Q+ ++ + V+ K E F++ + T V
Sbjct: 26 SQLTAFSSIVALAETPETSPAIGKVVIKETGEGGALLGDAVFELKNNTD-----GTTVSQ 80
Query: 75 STWNVNGLRACVKKNACVEYILEE 98
T G A Y L E
Sbjct: 81 RTEAQTG-EAIFSNIKPGTYTLTE 103
>2imq_X Salivary nitrophorin; ferrous heme, beta-sandwich, transport
protein; HET: HEM; 1.30A {Cimex lectularius} SCOP:
d.151.1.2 PDB: 1ntf_A* 1y21_A* 1yjh_A* 1si6_X*
Length = 282
Score = 27.5 bits (61), Expect = 5.3
Identities = 26/170 (15%), Positives = 44/170 (25%), Gaps = 23/170 (13%)
Query: 71 KVKVSTWNVNGLRACVKKNACVEYILEENPDIMALQQIRCQEDEVPESFRKSLSHYHMFW 130
V +WN RA + E PD++A+ +
Sbjct: 8 SVHTVSWNSGHERAPTNLEELLGLNSGETPDVIAVAVQGFGFQTDKPQQGPACVKNFQSL 67
Query: 131 IGSDK------GQ-GGVGLL--TKEKPL-------TVKYGIPGVSNQRGRV---ITAKFK 171
+ S +GL EK L + G + T K
Sbjct: 68 LTSKGYTKLKNTITETMGLTVYCLEKHLDQNTLKNETIIVTVDDQKKSGGIVTSFTIYNK 127
Query: 172 RFTFITVYVPNSGIKLKAIDFRMIWDQHFYDYIQSELRSNSNIIISGDLN 221
RF+F T + + + + + + + GDLN
Sbjct: 128 RFSFTTSRMSDEDVTSTNTKYAYDTRLDYSKKDD----PSDFLFWIGDLN 173
>2xsw_A 72 kDa inositol polyphosphate 5-phosphatase; inositol signalling,
SGC stockholm, structural genomics CONS hydrolase; 1.90A
{Homo sapiens}
Length = 357
Score = 27.6 bits (61), Expect = 6.2
Identities = 26/186 (13%), Positives = 57/186 (30%), Gaps = 41/186 (22%)
Query: 71 KVKVSTWNVNGLRACVKKNACVEYIL-----EENPDIMA--LQQIRCQEDEVPESFRKSL 123
+ V+TWN+ G + ++ L + D+ +Q+ E +++L
Sbjct: 27 ALFVATWNMQGQKE---LPPSLDEFLLPAEADYAQDLYVIGVQEGCSDRREWETRLQETL 83
Query: 124 S-HYHMFWIGSDKGQGGVGLL-----------TKEKPLTVKYGIPGVSNQRGRV---ITA 168
HY + + G + + ++ + TV I +G + T
Sbjct: 84 GPHYVLLSSAA---HGVLYMSLFIRRDLIWFCSEVECSTVTTRIVSQIKTKGALGISFTF 140
Query: 169 KFKRFTFITVYVP--NSGIKLKAIDFRMIWDQHFYDYIQSELRSNSN-----------II 215
F FIT + + + + +D+ + + +
Sbjct: 141 FGTSFLFITSHFTSGDGKVAERLLDYTRTVQALVLPRNVPDTNPYRSSAADVTTRFDEVF 200
Query: 216 ISGDLN 221
GD N
Sbjct: 201 WFGDFN 206
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 0.135 0.398
Gapped
Lambda K H
0.267 0.0604 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 5,011,849
Number of extensions: 297381
Number of successful extensions: 825
Number of sequences better than 10.0: 1
Number of HSP's gapped: 755
Number of HSP's successfully gapped: 45
Length of query: 327
Length of database: 6,701,793
Length adjustment: 94
Effective length of query: 233
Effective length of database: 4,077,219
Effective search space: 949992027
Effective search space used: 949992027
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: 57 (26.0 bits)