RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy6130
(295 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 = 300 bits (770), Expect = e-102
Identities = 113/282 (40%), Positives = 152/282 (53%), Gaps = 15/282 (5%)
Query: 16 KSSKKRKSEVEDSDANTKKTKSGSVENKATGPMNEKL-SLNKIDYSCNKKNKLGEEPNFK 74
+ K +E D + K K D K + G+ K
Sbjct: 4 RGKKGAVAEDGDELRTEPEAKKSKTAAKKNDKEAAGEGPALYEDPPDQKTSPSGKPATLK 63
Query: 75 IASWNVAGLRACVKKEGLDYIKKEDADIFCLQETKCHETQLPPEVKMKFPEYKTYWLSSP 134
I SWNV GLRA +KK+GLD++K+E DI CLQETKC E +LP E++ YW +
Sbjct: 64 ICSWNVDGLRAWIKKKGLDWVKEEAPDILCLQETKCSENKLPAELQELPGLSHQYWSAPS 123
Query: 135 -KAGYAGVGLYTKVKPNKVTYGLGTK-NEHYGRNC-----NSNIVNTFYIRKNVPNAGAG 187
K GY+GVGL ++ P KV+YG+G + ++ GR + +V + VPNAG G
Sbjct: 124 DKEGYSGVGLLSRQCPLKVSYGIGDEEHDQEGRVIVAEFDSFVLVTAY-----VPNAGRG 178
Query: 188 LKTLDKRLEWDKLFHEHLVKLDAEKPVILIGDLNVSHKPIDLANPTTNTRSAGFTIEERD 247
L L+ R WD+ F + L L + KP++L GDLNV+H+ IDL NP N ++AGFT +ER
Sbjct: 179 LVRLEYRQRWDEAFRKFLKGLASRKPLVLCGDLNVAHEEIDLRNPKGNKKNAGFTPQERQ 238
Query: 248 SFSSLLDK-GFTDSFRHLYPKRTGAYTYWSYMSKTARSRNTG 288
F LL DSFRHLYP AYT+W+YM ARS+N G
Sbjct: 239 GFGELLQAVPLADSFRHLYPNTPYAYTFWTYMMN-ARSKNVG 279
>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 = 293 bits (752), Expect = e-100
Identities = 111/241 (46%), Positives = 145/241 (60%), Gaps = 18/241 (7%)
Query: 58 DYSCNKKNKLGEEPNFKIASWNVAGLRACVKKEGLDYIKKEDADIFCLQETKCHETQLPP 117
D K + G+ KIASWNV GLRA +KK+GLD++K+E DI CLQETKC E +LP
Sbjct: 14 DPPDQKTSPSGKPATLKIASWNVDGLRAWIKKKGLDWVKEEAPDILCLQETKCSENKLPA 73
Query: 118 EVKMKFPEYKTYWLSSP-KAGYAGVGLYTKVKPNKVTYGLGTKNEHY---GRNC-----N 168
E++ YW + K GY+GVGL ++ P KV+YG+G +E + GR +
Sbjct: 74 ELQELPGLSHQYWSAPSDKEGYSGVGLLSRQCPLKVSYGIG--DEEHDQEGRVIVAEFDS 131
Query: 169 SNIVNTFYIRKNVPNAGAGLKTLDKRLEWDKLFHEHLVKLDAEKPVILIGDLNVSHKPID 228
+V Y VPNAG GL L+ R WD+ F + L L + KP++L GDLNV+H+ ID
Sbjct: 132 FVLVTA-Y----VPNAGRGLVRLEYRQRWDEAFRKFLKGLASRKPLVLCGDLNVAHEEID 186
Query: 229 LANPTTNTRSAGFTIEERDSFSSLLDK-GFTDSFRHLYPKRTGAYTYWSYMSKTARSRNT 287
L NP N ++AGFT +ER F LL DSFRHLYP AYT+W+YM ARS+N
Sbjct: 187 LRNPKGNKKNAGFTPQERQGFGELLQAVPLADSFRHLYPNTPYAYTFWTYMMN-ARSKNV 245
Query: 288 G 288
G
Sbjct: 246 G 246
>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 = 282 bits (723), Expect = 1e-95
Identities = 78/223 (34%), Positives = 117/223 (52%), Gaps = 15/223 (6%)
Query: 73 FKIASWNVAGLRACVKKEGLDYIKKEDADIFCLQETKCHETQLPPEVKMKFPEYKTYWLS 132
KI SWNV GLRA +K L + +E DI CLQE K QLP +++ Y++++
Sbjct: 4 LKIISWNVNGLRAVHRKGFLKWFMEEKPDILCLQEIKAAPEQLPRKLR-HVEGYRSFFTP 62
Query: 133 SPKAGYAGVGLYTKVKPNKVTYGLGTKN-EHYGRNC-----NSNIVNTFYIRKNVPNAGA 186
+ + GY+GV +YTKV P+ + G G + + GR + + N Y PN
Sbjct: 63 AERKGYSGVAMYTKVPPSSLREGFGVERFDTEGRIQIADFDDFLLYNI-Y----FPNGAM 117
Query: 187 GLKTLDKRLEWDKLFHEHLVKL-DAEKPVILIGDLNVSHKPIDLANPTTNTRSAGFTIEE 245
+ L +LE+ F E + + D+ + VI+ GD N +H+ IDLA P N+ +GF E
Sbjct: 118 SEERLKYKLEFYDAFLEDVNRERDSGRNVIICGDFNTAHREIDLARPKENSNVSGFLPVE 177
Query: 246 RDSFSSLLDKGFTDSFRHLYPKRTGAYTYWSYMSKTARSRNTG 288
R ++ G+ D+FR G YT+WSY ++ AR RN G
Sbjct: 178 RAWIDKFIENGYVDTFRMFNSD-PGQYTWWSYRTR-ARERNVG 218
>2jc5_A Exodeoxyribonuclease; hydrolase, repair phosphodiesterase, DNA
repair, exonuclease, endonuclease; HET: BCN DIO GOL;
1.50A {Neisseria meningitidis}
Length = 259
Score = 267 bits (685), Expect = 5e-90
Identities = 70/224 (31%), Positives = 117/224 (52%), Gaps = 16/224 (7%)
Query: 73 FKIASWNVAGLRACVKKEGLDYIKKEDADIFCLQETKCHETQLPPEVKMKFPEYKTYWLS 132
KI S NV G+R+ KK +YI ADI C+QE K E L ++K +W
Sbjct: 2 LKIISANVNGIRSAYKKGFYEYIAASGADIVCVQELKAQEADLSADMK-NPHGMHGHWHC 60
Query: 133 SPKAGYAGVGLYTKVKPNKVTYGLGTKN-EHYGRNC-----NSNIVNTFYIRKNVPNAGA 186
+ K GY+GV +Y+K KP+ V G+G + + GR ++++ Y +P+ +
Sbjct: 61 AEKRGYSGVAVYSKRKPDNVQIGMGIEEFDREGRFVRCDFGRLSVISL-Y----LPSGSS 115
Query: 187 GLKTLDKRLEWDKLFHEHLVKLDAE-KPVILIGDLNVSHKPIDLANPTTNTRSAGFTIEE 245
+ + + F+ L + E + +++ GD N++H+ IDL N N +++GF EE
Sbjct: 116 AEERQQVKYRFLDAFYPMLEAMKNEGRDIVVCGDWNIAHQNIDLKNWKGNQKNSGFLPEE 175
Query: 246 RDSFSSLLDK-GFTDSFRHLYPKRTGAYTYWSYMSKTARSRNTG 288
R+ ++ K G+TD +R LYP G YT+WS + A +++ G
Sbjct: 176 REWIGKVIHKLGWTDMWRTLYPDVPG-YTWWSNRGQ-AYAKDVG 217
>2j63_A AP-endonuclease; base excision repair, lyase; 2.48A {Leishmania
major}
Length = 467
Score = 238 bits (608), Expect = 5e-76
Identities = 72/349 (20%), Positives = 107/349 (30%), Gaps = 64/349 (18%)
Query: 3 PKKAAAKVVDKEEKSSKKRKSEVEDSDANTKKTKSGSVENKATGPMNEKLSLNKIDYSCN 62
+ + +T A E S
Sbjct: 80 GGAKKKATTGSPARRTSSAAKITNGDAGELIRTAEALAALNAKKSEKEIWSDVVPFVRRT 139
Query: 63 KKNKLGEEPNFKIASWNVAGLRACVKKEG---LDYIKKEDADIFCLQETKCHETQLPPEV 119
+ +K +WNVAGLR +KK +++ E D+ CLQETK + +
Sbjct: 140 TDSDFDPSRMYKFITWNVAGLRGLLKKNASALRAFMEAEKPDVLCLQETKLNVDEADANA 199
Query: 120 KMKFPE-YKTYWLSSP-KAGYAGVGLYTKVKPN------KVTYGLGTKNEHYGRNCNSNI 171
+ + Y K GY+G Y K + T G +E +
Sbjct: 200 TLGVVDGYSFVDHPCAFKRGYSGTRTYMKNSTTVKGLHARCTRGFALPSEPQADAAAGSR 259
Query: 172 VNTF--------YIRKN--------------------VPNAGAGLKTLDKRLE-WDKLFH 202
V + V N+G GL L R++ +D
Sbjct: 260 VLVEGAGDEEGRVLTTFLSPDPDSASSSSRIALVNTYVANSGMGLTRLPYRVQSFDPSMR 319
Query: 203 EHLVKLDAE-------------------KPVILIGDLNVSHKPID---LANPTTNTRSAG 240
E+L +LD I GDLNV+ + D + +G
Sbjct: 320 EYLHRLDTWATENAAVPSAAAMGSGSSPHGFIWAGDLNVAERDYDRYYAGTFKSMQECSG 379
Query: 241 FTIEERDSFSSLLDK-GFTDSFRHLYPKRTGAYTYWSYMSKTARSRNTG 288
F EER SF + + D FR LYP+ Y++WS R RN G
Sbjct: 380 FAPEERMSFRETMQRTNSVDIFRQLYPQAGPVYSFWSQRIN-GRPRNLG 427
>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 = 209 bits (535), Expect = 1e-67
Identities = 48/222 (21%), Positives = 86/222 (38%), Gaps = 25/222 (11%)
Query: 68 GEEPNFKIASWNVAGLRACVKKEGL-DYIKKEDADIFCLQETKCHETQLPPEVKMKFPEY 126
G + I + N+ GL + +K+ L +IK +D + C+QET K +
Sbjct: 3 GSNSHITILTLNINGLNSAIKRHRLASWIKSQDPSVCCIQETHLTCRDTHRL---KIKGW 59
Query: 127 KTYWLSSPKAGYAGVGLYTKVKPNKVTYGLGTKNE-HYGRNCNSNIVNTFYIRKNV--PN 183
+ + ++ K AGV + K + + E HY S I N+ PN
Sbjct: 60 RKIYQANGKQKKAGVAILVSDKTDFKPTKIKRDKEGHYIMVKGSIQQEELTIL-NIYAPN 118
Query: 184 AGAGLKTLDKRLEWDKLFHEHLVKLDAEKPVILIGDLNVSHKPIDLANPTTNTRSAGFTI 243
GA + K L + D + +++GD N +D + +
Sbjct: 119 TGAP--------RFIKQVLSDL-QRDLDSHTLIMGDFNTPLSTLDRSTRQKVNK------ 163
Query: 244 EERDSFSSLLDKGFTDSFRHLYPKRTGAYTYWSYMSKTARSR 285
+ ++ S+L D +R L+PK + YT++S S+
Sbjct: 164 DTQELNSALHQADLIDIYRTLHPK-STEYTFFSAPHH-TYSK 203
>1ako_A Exonuclease III; AP-endonuclease, DNA repair; 1.70A {Escherichia
coli} SCOP: d.151.1.1
Length = 268
Score = 161 bits (411), Expect = 1e-48
Identities = 59/237 (24%), Positives = 97/237 (40%), Gaps = 35/237 (14%)
Query: 74 KIASWNVAGLRACVKKEGLDYIKKEDADIFCLQETKCHETQLPPEVKMKFPE--YKTYWL 131
K S+N+ GLRA + ++K D+ LQETK H+ P E + Y ++
Sbjct: 2 KFVSFNINGLRARPHQL-EAIVEKHQPDVIGLQETKVHDDMFPLEE---VAKLGYNVFY- 56
Query: 132 SSPKAGYAGVGLYTKVKPNKVTYGLGTKNE---------HYGRNCNS-NIVNTFYIRKNV 181
+ G+ GV L TK P V G +E + ++N Y
Sbjct: 57 -HGQKGHYGVALLTKETPIAVRRGFPGDDEEAQRRIIMAEIPSLLGNVTVING-Y----F 110
Query: 182 PNAGAGLKTLDK---RLEWDKLFHEHLVK-LDAEKPVILIGDLNVSHKPIDLANPTTNTR 237
P G K + ++ + +L L + PV+++GD+N+S +D+ N +
Sbjct: 111 PQ-GESRDHPIKFPAKAQFYQNLQNYLETELKRDNPVLIMGDMNISPTDLDIGIGEENRK 169
Query: 238 SA------GFTIEERDSFSSLLDKGFTDSFRHLYPKRTGAYTYWSYMSKTARSRNTG 288
F EER+ L+ G D+FRH P+ ++++ Y SK N G
Sbjct: 170 RWLRTGKCSFLPEEREWMDRLMSWGLVDTFRHANPQTADRFSWFDYRSK-GFDDNRG 225
>2voa_A AF_EXO, XTHA, exodeoxyribonuclease III; EXOIII, AP endonuclease,
lyase; 1.7A {Archaeoglobus fulgidus}
Length = 257
Score = 141 bits (357), Expect = 1e-40
Identities = 62/229 (27%), Positives = 108/229 (47%), Gaps = 31/229 (13%)
Query: 74 KIASWNVAGLRA---CVKKEGLDYIKKEDADIFCLQETKCHETQLPPEVKMKFPE--YKT 128
KIA++NV +R+ V + ++K+ DI C+QETK + P F Y
Sbjct: 3 KIATFNVNSIRSRLHIV----IPWLKENKPDILCMQETKVENRKFPEAD---FHRIGYHV 55
Query: 129 YWLSSPKAGYAGVGLYTKVKPNKVTYGLGTKNEHYGR----NCNS-NIVNTFYIRKNVPN 183
+ S G GV + + +P V++GL ++ + R +++NT Y VP
Sbjct: 56 VFSGSK--GRNGVAIASLEEPEDVSFGLDSEPKDEDRLIRAKIAGIDVINT-Y----VPQ 108
Query: 184 AGAGLKTLDK---RLEWDKLFHEHLVK-LDAEKPVILIGDLNVSHKPIDLANPTTNTRSA 239
G + + +K +L+W + + +L K +D + GD+NV+ +PID+ +P
Sbjct: 109 -GFKIDS-EKYQYKLQWLERLYHYLQKTVDFRSFAVWCGDMNVAPEPIDVHSPDKLKNHV 166
Query: 240 GFTIEERDSFSSLLDKGFTDSFRHLYPKRTGAYTYWSYMSKTARSRNTG 288
F + R ++ +L+ GF D R ++P YT++ Y K A R G
Sbjct: 167 CFHEDARRAYKKILELGFVDVLRKIHPN-ERIYTFYDYRVKGAIERGLG 214
>2jc4_A Exodeoxyribonuclease III; hydrolase, repair phosphodiesterase, DNA
repair, exonuclease, endonuclease; HET: 1PE; 1.90A
{Neisseria meningitidis}
Length = 256
Score = 133 bits (338), Expect = 6e-38
Identities = 54/229 (23%), Positives = 85/229 (37%), Gaps = 31/229 (13%)
Query: 74 KIASWNVAGLRA---CVKKEGLDYIKKEDADIFCLQETKCHETQLPPEVKMKFPE--YKT 128
KI +WNV L V + + DI LQE K + + P +
Sbjct: 2 KITTWNVNSLNVRLPQV----QNLLADNPPDILVLQELKLDQDKFPAAA---LQMMGWHC 54
Query: 129 YWLSSPKAGYAGVGLYTKVKPNKVTYGL-GTKNEHYGR----NCNSNIVNTFYIRKNVPN 183
W Y GV + ++ P V +GL ++ R + V Y N
Sbjct: 55 VWSGQK--TYNGVAIVSRSVPQDVHFGLPALPDDPQRRVIAATVSGVRVINVY----CVN 108
Query: 184 AGAGLKTLDK---RLEWDKLFHEHLVK-LDAEKPVILIGDLNVSHKPIDLANPTTNTRSA 239
G L + K + +W E + + ++L+GD N++ D +P
Sbjct: 109 -GEALDS-PKFKYKEQWFAALTEFVRDEMTRHGKLVLLGDFNIAPADADCYDPEKWHEKI 166
Query: 240 GFTIEERDSFSSLLDKGFTDSFRHLYPKRTGAYTYWSYMSKTARSRNTG 288
+ ER F +LLD G TDS R ++P+ YT++ Y R G
Sbjct: 167 HCSSVERQWFQNLLDLGLTDSLRQVHPE-GAFYTWFDYRGA-MFQRKLG 213
>1wdu_A TRAS1 ORF2P; four-layered alpha/beta sandwich, RNA binding protein;
2.40A {Bombyx mori} SCOP: d.151.1.1
Length = 245
Score = 88.1 bits (217), Expect = 7e-21
Identities = 20/211 (9%), Positives = 52/211 (24%), Gaps = 16/211 (7%)
Query: 59 YSCNKKNKLGEEPNFKIASWNVAGLRACVKKEGLDYIKKEDADIFCLQETKCHETQLPPE 118
++ K + P +++ N+ + E A I +QE +
Sbjct: 6 WNTTAKVRPKNGPPYRVLQANLQRKKLA-TAELAIEAATRKAAIALIQEPYVGGAKSM-- 62
Query: 119 VKMKFPEYKTYWLSSPKAGYAGVGLYTKVKPNKVTYGLGTKNEHY-GRNCNSNIVNTFYI 177
F + + ++ G + V + + +
Sbjct: 63 --KGFRGVRVFQSTAQGDGTVKAAIAVFDHDLDVIQYPQLTTNNIVVVGIRTRAWEITLV 120
Query: 178 RKNVPNAGAGLKTLDKRLEWDKLFHEHLVKLDAEKPVILIGDLNVSHKPIDLANPTTNTR 237
L++ ++ +I GD N + + R
Sbjct: 121 SYYFEPDKPIESYLEQIKRVERKMGPK--------RLIFGGDANAKS--TWWGSKEDDAR 170
Query: 238 SAGFTIEERDSFSSLLDKGFTDSFRHLYPKR 268
+ +L++G +F + +
Sbjct: 171 GDQLMGTLGELGLHILNEGDVPTFDTIRGGK 201
>3teb_A Endonuclease/exonuclease/phosphatase; PSI-biology, MCSG, midwest
center for structural genomics; 2.99A {Leptotrichia
buccalis c-1013-b}
Length = 266
Score = 60.3 bits (146), Expect = 7e-11
Identities = 34/232 (14%), Positives = 66/232 (28%), Gaps = 47/232 (20%)
Query: 74 KIASWNVAGLRACVKKEGLD----YIKKEDADIFCLQETKCHETQLPPEVKMKF------ 123
KI + NV + E +D I ++ D+ +QE ++
Sbjct: 5 KILTVNVHAWLEENQMEKIDILARTIAEKQYDVIAMQEVNQLMNNKIIFDDIREENYAWV 64
Query: 124 ----------PEYKTYWLSSP---KAGYAGVGLYTKVKPNKVTYGLGTKNEHYG----RN 166
+Y +W +S GV + T+ K T + R
Sbjct: 65 LLETLQKYTDTDYYLHWSNSHIGFGKYNEGVAVITRHKIKAEDEFYCTFAQSVRTISARR 124
Query: 167 CNSNIVNTFYIRKNVPNAGAGLKTLDKRLEWDKLFHEHLVKLDAEKPVILIGDLNVSHKP 226
S +N + L + + L + IL+GD N
Sbjct: 125 IVSITINYEGQDIEFYSCHMNLPNCETEDMGKNI-QTILNRTQNSNLKILMGDFN----- 178
Query: 227 IDLANPTTNTRSAGFTIEERDSFSSLLDKGFTDSFRHLYPKRTGAYTYWSYM 278
+ N ++ ++L +G D++ + K+ T +
Sbjct: 179 ---TDAIGNV----------AAYENILSQGLFDTYV-MAEKKDDGITVDKSI 216
>3g6s_A Putative endonuclease/exonuclease/phosphatase family protein;
alpha-beta protein, structural genomics, PSI-2; 2.50A
{Bacteroides vulgatus atcc 8482}
Length = 267
Score = 49.2 bits (117), Expect = 4e-07
Identities = 29/234 (12%), Positives = 64/234 (27%), Gaps = 52/234 (22%)
Query: 72 NFKIASWNVAGLRACVKKEG-----------LDYIKKEDADIFCLQETKCHETQLPPEVK 120
+ + A++N+ R ++ +IK + DI +QE ++ Q
Sbjct: 3 DVRWATFNI---RYDNPQDSLNNWQYRKDRVCQFIKDHELDIVGMQEVLHNQFQDLRAGL 59
Query: 121 MKFPEYKTYWLSSPKAGYAGVGLYTKVKPNKVTYG----------LGTKNEHYGRNCNSN 170
++ AG Y K K + +G +
Sbjct: 60 PEYDGIGVGRDDGKTAGEYAPLFYRKDKYEVLDSNTFWLAENPDSVGMMGWDAVCVRIAT 119
Query: 171 IVNTFYIRKNVPNAGAGLKTLD-----KRLEWDKLFHEHLVKLDAEKPVILIGDLNVSHK 225
F + A D R + L + ++ E+P ++ GD N
Sbjct: 120 WA-KFKDKATGKIFMAVNTHFDHVGEEARRQSALLIIRKIKEIVGERPAVVTGDFN---- 174
Query: 226 PIDLANPTTNTRSAGFTIEERDSFSSLLDKG--FTDSFRHLYPKRTGAYTYWSY 277
++ + ++ D+++ YT+ +
Sbjct: 175 ----VTDASDA------------YETITTNEFVMKDAYKTAARVTGVDYTFHDF 212
>2ei9_A Non-LTR retrotransposon R1BMKS ORF2 protein; four layered alpha
beta sandwich, gene regulation; 2.00A {Bombyx mori}
Length = 240
Score = 45.4 bits (106), Expect = 7e-06
Identities = 24/216 (11%), Positives = 56/216 (25%), Gaps = 40/216 (18%)
Query: 70 EPNFKIASWNVAGLRACVKKEGLDYIKKEDADIFCLQETKCHETQLPPEVKMKFPEYKTY 129
P +I N+ G +E + DI +QE Y
Sbjct: 5 RPRLRIGQINLGGAED-ATRELPSIARDLGLDIVLVQEQ-----------------YSMV 46
Query: 130 WLSSPKAGYAGVGLYTKVKPNKVTYGLGTKNEHYG----RNCNSNIVNTFYIRKNVPNAG 185
+ + G+Y + + + H + +V+ Y + + P
Sbjct: 47 GFLAQCGAHPKAGVYIRNRVLPCAVLHHLSSTHITVVHIGGWDLYMVS-AYFQYSDP--- 102
Query: 186 AGLKTLDKRLEWDKLFHEHLVKLDAEKPVILIGDLNVSHKPIDLANPTTNTRSAGFTIEE 245
++ +++ V++ D N +H P+ + P +
Sbjct: 103 ---------IDPYLHRLGNILDRLRGARVVICADTN-AHSPLWHSLPRHYVGRGQEVADR 152
Query: 246 RDSFSSLLDKGFTDSFRHLYPKRTGAYTYWSYMSKT 281
R + T+ + ++
Sbjct: 153 RAKMEDFIG---ARRLVVHNA-DGHLPTFSTANGES 184
>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 = 43.5 bits (102), Expect = 3e-05
Identities = 41/238 (17%), Positives = 69/238 (28%), Gaps = 58/238 (24%)
Query: 72 NFKIASWNVAGLRACVKKEG-------------LDYIKKEDADIFCLQETKCHETQLPPE 118
+ +AS+N+ R + ++ D DIF QE C QL +
Sbjct: 6 SLTVASYNL---RNANGSDSARGDGWGQRYPVIAQMVQYHDFDIFGTQE--CFLHQL-KD 59
Query: 119 VKMKFPEYKTYWLSSPKAGYAGVG---LYTKVKPNKVTYG---LGTKNEHYGRNCNSNIV 172
+K P Y + G Y K + V G L + + ++ +
Sbjct: 60 MKEALPGYDYIGVGRDDGKDKGEHSAIFYRTDKFDIVEKGDFWLSETPDVPSKGWDAVLP 119
Query: 173 NTFYI----------RKNVPNAGAGLKTLDKRLEWDKLFHEHLVKLDAEK--PVILIGDL 220
N R+E L E + +L K P IL GD
Sbjct: 120 RICSWGHFKCKDTGFEFLFFNLHMDHIGKKARVESAFLVQEKMKELGRGKNLPAILTGDF 179
Query: 221 NVSHKPIDLANPTTNTRSAGFTIEERDSFSSLLDKG-FTDSFRHLYPKRTGAYTYWSY 277
N + S+ + + KG DS+ + T+ ++
Sbjct: 180 N--------------------VDQTHQSYDAFVSKGVLCDSYEKCDYRYALNGTFNNF 217
>3i41_A Beta-hemolysin; beta toxin, sphingomyelinase, toxin; 1.75A
{Staphylococcus aureus} PDB: 3i46_A 3i48_A 3i5v_A*
3k55_A
Length = 317
Score = 43.2 bits (101), Expect = 5e-05
Identities = 33/241 (13%), Positives = 79/241 (32%), Gaps = 43/241 (17%)
Query: 69 EEPNFKIASWNVAGLRACVKKEG---------LDYIKKEDADIFCLQETKCHET--QLPP 117
++ + K+ S NV L + ++ D+ E + +L
Sbjct: 26 DDTDLKLVSHNVYMLSTVLYPNWGQYKRADLIGQSSYIKNNDVVIFNEAFDNGASDKLLS 85
Query: 118 EVKMKFPEYKTYWLSSPKAGY--------------AGVGLYTK---VKPNKVTYGLGTKN 160
VK ++P Y+T L ++G+ GV + +K + + + G
Sbjct: 86 NVKKEYP-YQTPVLGRSQSGWDKTEGSYSSTVAEDGGVAIVSKYPIKEKIQHVFKSGCGF 144
Query: 161 EHYGR-----------NCNSNIVNT-FYIRKNVPNAGAGLKTLDKRLEWDKLFHEHLVKL 208
++ N +++ T + AG K ++++ F + +
Sbjct: 145 DNDSNKGFVYTKIEKNGKNVHVIGTHTQSEDSRCGAGHDRKIRAEQMKEISDFVKKK-NI 203
Query: 209 DAEKPVILIGDLNVSHKPIDLANPTTNTRSAGFTIE-ERDSFSSLLDKGFTDSFRHLYPK 267
++ V + GDLNV+ + + N ++ + ++ + P+
Sbjct: 204 PKDETVYIGGDLNVNKGTPEFKDMLKNLNVNDVLYAGHNSTWDPQSNSIAKYNYPNGKPE 263
Query: 268 R 268
Sbjct: 264 H 264
>3l1w_A Uncharacterized protein; APC29019.2, conserved protein,
enterococcus faecalis V583, PSI-2, MCSG, structural
genomics; 1.60A {Enterococcus faecalis}
Length = 257
Score = 42.7 bits (100), Expect = 6e-05
Identities = 30/172 (17%), Positives = 48/172 (27%), Gaps = 29/172 (16%)
Query: 74 KIASWNVAGLRACVKKEG-----------LDYIKKEDADIFCLQETKCHETQLPPEVKMK 122
KIA++NV R + + I D + C+QE Q+
Sbjct: 2 KIATYNV---RVDTEYDQDWQWSFRKEAVCQLINFHDWSLCCIQE--VRPNQVRDLKAYT 56
Query: 123 FPEYKTYWLSSPKAGYAGVGLYTKVKPNKVTYG---LGTKNEHYGRNCNSNIVNTFYI-- 177
+ G LY + K + G L + + +
Sbjct: 57 TFTCLSAEREGDGQGEGLAILYNEQKVQAIDTGYFWLSETPQQPSIHPEAGCPRIALWGL 116
Query: 178 --------RKNVPNAGAGLKTLDKRLEWDKLFHEHLVKLDAEKPVILIGDLN 221
V N + RL + E L A+ P +L+GD N
Sbjct: 117 FKETTQNTPFLVINVHLDHISAHARLAGMTVILEELHDKIAQYPTLLMGDFN 168
>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 = 27/156 (17%), Positives = 47/156 (30%), Gaps = 27/156 (17%)
Query: 118 EVKMKFPEYKTYWLS-----SPKAGYAGV-GLYTKVKPNKVTYGLGTKNEHYGRNCNSNI 171
+V+ K +K +WL+ SP+ + L ++ PN + + N +
Sbjct: 175 KVQCKMD-FKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAE 233
Query: 172 VNTFYIRKNVPNAGAGLKTLDKRLEWDKLFHEHLVKLDAE-KPVILIGDLNVSHKPIDLA 230
+ K N L L + + + K ++ V D
Sbjct: 234 LRRLLKSKPYENC---LLVLLN--VQNA---KAWNAFNLSCKILLTTRFKQV----TDFL 281
Query: 231 NPTTNTR------SAGFTIEERDS-FSSLLDKGFTD 259
+ T T S T +E S LD D
Sbjct: 282 SAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQD 317
Score = 39.1 bits (90), Expect = 0.002
Identities = 33/181 (18%), Positives = 58/181 (32%), Gaps = 50/181 (27%)
Query: 54 LNKIDYSCNKKNKLGEEPNFKIASWNVAG----LRACVKKEGLDYIKKEDAD------IF 103
+ Y K E F + +++ ++ + KE +D+I +F
Sbjct: 11 TGEHQY-QYKDILSVFEDAF-VDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTLRLF 68
Query: 104 CLQETKCHETQLPPEVKMKF------PEYKTYWLSSPKAGYAGVGLYTKVKPNKVTYGLG 157
+K E+ KF YK +L SP K + + +
Sbjct: 69 WTLLSK------QEEMVQKFVEEVLRINYK--FLMSP----------IKTEQRQPSMMTR 110
Query: 158 TKNEHYGRNCNSNIVNTFYIRKNVPNAGAGLKTLDKRLEWDKLFHEHLVKLDAEKPVILI 217
E R N N V + + NV RL+ + L++L K V++
Sbjct: 111 MYIEQRDRLYNDNQV---FAKYNVS-----------RLQPYLKLRQALLELRPAKNVLID 156
Query: 218 G 218
G
Sbjct: 157 G 157
Score = 29.4 bits (65), Expect = 1.6
Identities = 30/218 (13%), Positives = 57/218 (26%), Gaps = 68/218 (31%)
Query: 89 KEGLDYIKKEDADIFCLQETKCHETQLPPEVKMKFPEYKTYWLSSPKAGYAGVGLYTKVK 148
L E + L+ C LP EV ++P+ + + +
Sbjct: 295 SMTLT--PDEVKSLL-LKYLDCRPQDLPREVL----------TTNPRR-LSIIAESIRDG 340
Query: 149 PNKVTYGLGTKNEHYGRNCNSNIVNTFY-------IRK------------NVPNAGAGLK 189
+H + + I+ + RK ++P
Sbjct: 341 LATWDN-----WKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIP-----TI 390
Query: 190 TLDKRLEW------------DKLFHEHLVKLDAEKPVILIGDLNVSHKPIDLANPTTNTR 237
L + W +KL LV+ ++ I I + ++L N
Sbjct: 391 LL-SLI-WFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIY-----LELKVKLENEY 443
Query: 238 SAGFTIEERDSFSSLLDKGFTDSFRHLYPKRTGAYTYW 275
+ +I + + D L P Y Y
Sbjct: 444 ALHRSIVDHYNIPKTFDSD------DLIPPYLDQYFYS 475
>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 = 14/99 (14%), Positives = 28/99 (28%), Gaps = 12/99 (12%)
Query: 69 EEPNFKIASWNVAGLRACVKKEG---------LDYIKKEDADIFCLQETKCHET--QLPP 117
+ K+ + NV L + ++ D+ L E + +L
Sbjct: 6 QNDTLKVMTHNVYMLSTNLYPNWGQTERADLIGAADYIKNQDVVILNEVFDNSASDRLLG 65
Query: 118 EVKMKFPEYKTYWLSSPKAGYAGVGLYTKVKPNKVTYGL 156
+K ++P +T L L G+
Sbjct: 66 NLKKEYP-NQTAVLGRSSGSEWDKTLGNYSSSTPEDGGV 103
>1zwx_A SMCL, sphingomyelinase-C; dnase1-like fold, beta-hairpin,
hydrolase; 1.90A {Listeria ivanovii} SCOP: d.151.1.3
Length = 301
Score = 41.2 bits (96), Expect = 2e-04
Identities = 31/242 (12%), Positives = 73/242 (30%), Gaps = 44/242 (18%)
Query: 69 EEPNFKIASWNVAGLRACVKKEG---------LDYIKKEDADIFCLQETKCHET--QLPP 117
NFKI S NV + ++ D+ L E +L
Sbjct: 7 YPGNFKITSHNVYLFSRNIYPNWGQMHRADLIAQADYMKNNDVVILNEAFDTSASHRLLN 66
Query: 118 EVKMKFPEYKTYWLSSPKAGY--------------AGVGLYTK---VKPNKVTYGLGTKN 160
++ +P ++T + K G+ GV + ++ V+ ++ + G
Sbjct: 67 NLREMYP-HQTPVIGRSKHGWDKTEGNYSNFALEDGGVAVVSQWPIVEKSQHIFQRGGGA 125
Query: 161 EHYGR-----------NCNSNIVNT-FYIRKNVPNAGAGLKTLDKRLEWDKLFHEHLVKL 208
+ +I+ T ++ + ++++ + F +
Sbjct: 126 DRLSNKGFAYVKIMKNGKPYHIIGTHTQADDSLISKDTSRAIRAEQMQEIQTFIAKK-NI 184
Query: 209 DAEKPVILIGDLNV--SHKPIDLANPTTNTRSAGFTIEERDSFSSLLDKGFTDSFRHLYP 266
++ + + GDLNV N S + ++ + +S+ P
Sbjct: 185 PKDEIIFIGGDLNVNYGTDEYHDMLKLLNVSSPANFNGQMATWDPTTNSMLKESYPKAAP 244
Query: 267 KR 268
+
Sbjct: 245 EY 246
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 35.1 bits (80), Expect = 0.014
Identities = 19/108 (17%), Positives = 41/108 (37%), Gaps = 40/108 (37%)
Query: 6 AAAKVVDKEEKSSKK----RKSEVEDSDANTKKTKSGSVENKATGPM-------NEKLSL 54
A A + +E +S +K ++ +++ DA +K + E KA + +E++
Sbjct: 75 AQADRLTQEPESIRKWREEQRKRLQELDAASKVMEQEWRE-KAKKDLEEWNQRQSEQVEK 133
Query: 55 NKIDYSCNKKNKLGEEPNFKIASWNVAGLRACVKKEGLDYIKKEDADI 102
NK N++ ++ + ++ DADI
Sbjct: 134 NK------INNRIADK----------------------AFYQQPDADI 153
>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 = 32.4 bits (73), Expect = 0.13
Identities = 26/172 (15%), Positives = 46/172 (26%), Gaps = 21/172 (12%)
Query: 73 FKIASWNV--AGLRACVKKEGLDYIKK--EDADIFCLQETKCHETQLPPEVKMKFPEYKT 128
KIA++N+ G YI + DI +QE + ++ +
Sbjct: 1 LKIAAFNIRTFGETKMSNATLASYIVRIVRRYDIVLIQEVRDSHLVAVGKLLDYLNQDDP 60
Query: 129 Y---WLSSPKAG-------YAGVGLYTKVKPNKVTYGLGTKNEHYGRNCN-SNIVNTFYI 177
++ S G Y + KV + + V F
Sbjct: 61 NTYHYVVSEPLGRNSYKERYLFLFRPNKVSVLDTYQYDDGCESCGNDSFSREPAVVKFSS 120
Query: 178 RKNVPN----AGAGLKTLDKRLEWDKL--FHEHLVKLDAEKPVILIGDLNVS 223
D E + L + + + V+L+GD N
Sbjct: 121 HSTKVKEFAIVALHSAPSDAVAEINSLYDVYLDVQQKWHLNDVMLMGDFNAD 172
>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 = 32.3 bits (73), Expect = 0.24
Identities = 24/136 (17%), Positives = 45/136 (33%), Gaps = 41/136 (30%)
Query: 5 KAAAKVVDKEEKSSKKR----KSEVEDSDANTKKTKSGSVENKATGPMNEKLSLNKIDYS 60
++ +VV R + V + ++ G + S + Y
Sbjct: 1780 ESLVEVV-------FYRGMTMQVAVPRDELGRSNYGMIAI---NPGRVAASFSQEALQYV 1829
Query: 61 CNK-KNKLGE--EP-NFKIASWNVAG--------LRACVKK--EGLDYIKKEDADIFCLQ 106
+ + G E N+ NV LRA + L++IK + DI LQ
Sbjct: 1830 VERVGKRTGWLVEIVNY-----NVENQQYVAAGDLRA-LDTVTNVLNFIKLQKIDIIELQ 1883
Query: 107 ETKCHETQLPPEVKMK 122
++ L E +++
Sbjct: 1884 KS------LSLE-EVE 1892
Score = 31.6 bits (71), Expect = 0.40
Identities = 20/113 (17%), Positives = 38/113 (33%), Gaps = 25/113 (22%)
Query: 161 EHYGRNCNSNIVNTFYIRKNVPNAGAGLKTL-------------DKRLEWDKLFHEHLVK 207
+ YG + +IV + + G K + D +L+ +K+F E
Sbjct: 1655 DTYGFSI-LDIVINNPVNLTIHFGGEKGKRIRENYSAMIFETIVDGKLKTEKIFKE---- 1709
Query: 208 LDAEKPVILIGDLNVSHKPIDLANPTTNTRSAGFTIEERDSFSSLLDKGFTDS 260
++ L + T T+ A + E+ +F L KG +
Sbjct: 1710 INEHSTSYTFRS------EKGLLSATQFTQPALTLM-EKAAFEDLKSKGLIPA 1755
>2yrb_A Protein fantom; beta sandwich, NPPSFA, national project on protein
structural and functional analyses; NMR {Homo sapiens}
SCOP: b.7.1.1
Length = 156
Score = 26.9 bits (59), Expect = 6.4
Identities = 11/45 (24%), Positives = 15/45 (33%)
Query: 84 RACVKKEGLDYIKKEDADIFCLQETKCHETQLPPEVKMKFPEYKT 128
+ E L ++ FC E Q P V+ PEY
Sbjct: 26 KVTFSSEVLQASGDKEPVTFCTYAFYDFELQTTPVVRGLHPEYNF 70
>3v2u_C Protein GAL3; rossmann fold, GHMP superfamily, transcription
regulation, transcription; HET: GLA ATP; 2.10A
{Saccharomyces cerevisiae} PDB: 3v5r_A 2aj4_A*
Length = 520
Score = 27.0 bits (59), Expect = 7.7
Identities = 6/33 (18%), Positives = 11/33 (33%)
Query: 205 LVKLDAEKPVILIGDLNVSHKPIDLANPTTNTR 237
+L + +I + V + A N R
Sbjct: 237 FPQLKNHEISFVIANTLVKSNKFETAPTNYNLR 269
>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 = 26.7 bits (59), Expect = 9.5
Identities = 12/76 (15%), Positives = 18/76 (23%), Gaps = 6/76 (7%)
Query: 75 IASWNVAGLRACVKKEGLDYIKKEDADI--FCLQETKCHETQLPPEVKMKFPEYKTYWLS 132
++NV G + D+ QE + W
Sbjct: 12 AGTYNVNGQSPKECLRLWLSNGIQAPDVYCVGFQELDL----SKEAFFFHDTPKEEEWFK 67
Query: 133 SPKAGYAGVGLYTKVK 148
+ G Y KVK
Sbjct: 68 AVSEGLHPDAKYAKVK 83
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
0.312 0.130 0.388
Gapped
Lambda K H
0.267 0.0502 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 4,319,298
Number of extensions: 244234
Number of successful extensions: 473
Number of sequences better than 10.0: 1
Number of HSP's gapped: 426
Number of HSP's successfully gapped: 32
Length of query: 295
Length of database: 6,701,793
Length adjustment: 93
Effective length of query: 202
Effective length of database: 4,105,140
Effective search space: 829238280
Effective search space used: 829238280
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 57 (26.3 bits)