RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 039703
(284 letters)
>2h56_A DNA-3-methyladenine glycosidase; 10174367, EC 3.2.2.-, struc
genomics, PSI-2, protein structure initiative, joint
center structural genomics; 2.55A {Bacillus halodurans}
Length = 233
Score = 252 bits (645), Expect = 1e-84
Identities = 68/194 (35%), Positives = 103/194 (53%), Gaps = 1/194 (0%)
Query: 72 ALRHLRDKDPLLATLIDAHRPPTFESSRSPFLSLAKSILYQQLAYKAAKSIYTRFVALFN 131
++ + +D L I+ + +PF SL SI+ QQL+ KAA +IY R L
Sbjct: 22 EVKTIVAQDSRLFQFIEIAGEVQLPTKPNPFQSLVSSIVEQQLSIKAASAIYGRVEQLV- 80
Query: 132 GEDNILPDAVLAVSPQQLREIGVSYRKASYLRDLAEKYTDGILSDESIVEMDDVTMFKML 191
G P+ + VS + LR+ GVS RK Y+R + E G L + + T+ + L
Sbjct: 81 GGALEKPEQLYRVSDEALRQAGVSKRKIEYIRHVCEHVESGRLDFTELEGAEATTVIEKL 140
Query: 192 TSVKGIGAWSVHMFMIFSLHKPDVLPVGDLGVRKGLQVLYGLKELPGALKMEEVCEKWKP 251
T++KGIG W+ MFM+FSL + DVL VGD+G+++G + LYG E G + + W P
Sbjct: 141 TAIKGIGQWTAEMFMMFSLGRLDVLSVGDVGLQRGAKWLYGNGEGDGKKLLIYHGKAWAP 200
Query: 252 YRSVGSWYMWRLME 265
Y +V Y+W+
Sbjct: 201 YETVACLYLWKAAG 214
>3s6i_A DNA-3-methyladenine glycosylase 1; DNA glycosylase, DNA repair,
helix-hairpin-helix (HHH), ABAS tetrahydrofuran (THF);
HET: 3DR; 2.28A {Schizosaccharomyces pombe}
Length = 228
Score = 244 bits (624), Expect = 2e-81
Identities = 59/201 (29%), Positives = 104/201 (51%), Gaps = 4/201 (1%)
Query: 72 ALRHLRDKDPLLATLIDA---HRPPTFESSRSPFLSLAKSILYQQLAYKAAKSIYTRFVA 128
A HL D L+ +RP + P+ L +++ QQL KAA +I+ RF +
Sbjct: 18 AEIHLSGLDENWKRLVKLVGNYRPNRSMEKKEPYEELIRAVASQQLHSKAANAIFNRFKS 77
Query: 129 LFNGEDNILPDAVLAVSPQQLREIGVSYRKASYLRDLAEKYTDGIL-SDESIVEMDDVTM 187
+ N P+ + + + +R G S RK L+ +AE G++ + E + + +
Sbjct: 78 ISNNGQFPTPEEIRDMDFEIMRACGFSARKIDSLKSIAEATISGLIPTKEEAERLSNEEL 137
Query: 188 FKMLTSVKGIGAWSVHMFMIFSLHKPDVLPVGDLGVRKGLQVLYGLKELPGALKMEEVCE 247
+ LT +KGIG W+V M +IFSL++ DV+P DL +R G + L+ L ++P + + + E
Sbjct: 138 IERLTQIKGIGRWTVEMLLIFSLNRDDVMPADDLSIRNGYRYLHRLPKIPTKMYVLKHSE 197
Query: 248 KWKPYRSVGSWYMWRLMEAKG 268
P+R+ +WY+W+ +
Sbjct: 198 ICAPFRTAAAWYLWKTSKLAD 218
>2yg9_A DNA-3-methyladenine glycosidase II, putative; hydrolase, DNA
repair; 1.95A {Deinococcus radiodurans} PDB: 2yg8_A
Length = 225
Score = 222 bits (569), Expect = 3e-73
Identities = 63/192 (32%), Positives = 100/192 (52%), Gaps = 11/192 (5%)
Query: 72 ALRHLRDKDPLLATLIDAHRP-PTFESSRSPFLSLAKSILYQQLAYKAAKSIYTRFVALF 130
A+ HL +DP+LA + P + PF L +S+ QQL+ KAA++IY R L
Sbjct: 32 AVAHLS-RDPVLAQVTSLCGELPVLAPTPDPFGRLVRSVAGQQLSVKAAQAIYGRLEGLP 90
Query: 131 NGEDNILPDAVLAVSPQQLREIGVSYRKASYLRDLAEKYTDGILSDESIVEMDDVTMFKM 190
++P A+L VS LR +G+S+ K ++ A G + + D +
Sbjct: 91 G---GVVPAALLKVSGDDLRGVGLSWAKVRTVQAAAAAAVSGQIDFAHLSGQPDELVIAE 147
Query: 191 LTSVKGIGAWSVHMFMIFSLHKPDVLPVGDLGVRKGLQVLYGLKELPGALKMEEVCEKWK 250
L + GIG W+ MF++F+L +PDV GDL +R+G++ LY ++ +V +W
Sbjct: 148 LVQLPGIGRWTAEMFLLFALARPDVFSSGDLALRQGVERLYPGED------WRDVTARWA 201
Query: 251 PYRSVGSWYMWR 262
PYRS+ S Y+W
Sbjct: 202 PYRSLASRYLWA 213
>2jhn_A ALKA, 3-methyladenine DNA-glycosylase; DNA repair,
N1-methyladenine, N3-methylcytosine, hyperthermophiles,
hydrolase; HET: MBO MES; 1.8A {Archaeoglobus fulgidus}
PDB: 2jhj_A
Length = 295
Score = 196 bits (499), Expect = 1e-61
Identities = 54/206 (26%), Positives = 94/206 (45%), Gaps = 20/206 (9%)
Query: 70 DIALRHLRDKDPLLATLIDAH---RPPTFESSRSPFLSLAKSILYQQLAYKAAKSIYTRF 126
L D D L L + S S F +AK+I+ QQ+++ A+ + +
Sbjct: 85 PEELYRFMDGDEKLRMLKNRFYGFGRAGL-MSMSVFEGIAKAIIQQQISFVVAEKLAAKI 143
Query: 127 VALFNGEDN---------ILPDAVLAVSPQQLREIGVSYRKASYLRDLAEKYTDGILSDE 177
V F E +A+L + LRE G+S RKA + ++A++ + E
Sbjct: 144 VGRFGDEVEWNGLKFYGFPTQEAILKAGVEGLRECGLSRRKAELIVEIAKE-----ENLE 198
Query: 178 SIVEMDDVTMFKMLTSVKGIGAWSVHMFMIFSLHKPDVLPVGDLGVRKGLQVLYGLKELP 237
+ E + ++ LTS KGIG W+ + + +L +V P DLGVR+ + LY E+
Sbjct: 199 ELKEWGEEEAYEYLTSFKGIGRWTAELVLSIALG-KNVFPADDLGVRRAVSRLYFNGEIQ 257
Query: 238 GALKMEEVC-EKWKPYRSVGSWYMWR 262
A K+ E+ E++ + +Y++
Sbjct: 258 SAEKVREIARERFGRFARDILFYLFL 283
>1mpg_A ALKA, 3-methyladenine DNA glycosylase II; DNA repair, base
excision, methylation, ALK hydrolase; 1.80A {Escherichia
coli} SCOP: a.96.1.3 d.129.1.2 PDB: 1diz_A 1pvs_A*
3cvs_A* 3cvt_A* 3cw7_A* 3cwa_A* 3cws_A* 3cwt_A* 3cwu_A*
3d4v_A* 3ogd_A* 3oh9_A* 3oh6_A*
Length = 282
Score = 180 bits (459), Expect = 7e-56
Identities = 40/196 (20%), Positives = 71/196 (36%), Gaps = 17/196 (8%)
Query: 80 DPLLATLIDAHRPPTFESSRSPFLSLAKSILYQQLAYKAAKSIYTRFVALFNGEDN---- 135
+ L L A F ++IL Q ++ A + R L+ +
Sbjct: 92 NGALGRLGAARPGLRLPGCVDAFEQGVRAILGQLVSVAMAAKLTARVAQLYGERLDDFPE 151
Query: 136 ----ILPDAVLAVSPQQLREIGVSYRKASYLRDLAEKYTDGILSDESIVEMDDVTMFKML 191
P + A PQ L+ +G+ ++A L LA +G L + D K L
Sbjct: 152 YICFPTPQRLAAADPQALKALGMPLKRAEALIHLANAALEGTLPMT--IPGDVEQAMKTL 209
Query: 192 TSVKGIGAWSVHMFMIFSLHKPDVLPVGDLGVRKGLQVLYGLKELPGALKMEEVCEKWKP 251
+ GIG W+ + F + DV D +++ + ++ E+WKP
Sbjct: 210 QTFPGIGRWTANYFALRGWQAKDVFLPDDYLIKQRFPGM-------TPAQIRRYAERWKP 262
Query: 252 YRSVGSWYMWRLMEAK 267
+RS ++W +
Sbjct: 263 WRSYALLHIWYTEGWQ 278
>3i0w_A 8-oxoguanine-DNA-glycosylase; OGG, cacogg, DNA, 8-OXOG, 8OXOG,
glycosylase, cytosine, hydrolase,lyase/DNA complex; HET:
8OG; 1.73A {Clostridium acetobutylicum} PDB: 3i0x_A*
3f10_A* 3f0z_A
Length = 290
Score = 151 bits (383), Expect = 2e-44
Identities = 39/200 (19%), Positives = 69/200 (34%), Gaps = 12/200 (6%)
Query: 73 LRHLRDKDPLLATLIDAHRPPTFESSRSPFLSLAKSILYQQLAYKAAKSIYTRFVALFNG 132
++ +DPLL +D + PF L I+ K
Sbjct: 88 IKKELSRDPLLKKSVDFG-EGIRILRQDPFEILLSFIISANNRIPMIKKCINNISEKAGK 146
Query: 133 EDN---------ILPDAVLAVSPQQLREIGVSYRKASYLRDLAEKYTDGILSDESIVEMD 183
+ D + + + E +R A YL+D ++ +G L+ E I ++
Sbjct: 147 KLEYKGKIYYAFPTVDKLHEFTEKDFEECTAGFR-AKYLKDTVDRIYNGELNLEYIKSLN 205
Query: 184 DVTMFKMLTSVKGIGAWSVHMFMIFSLHKPDVLPVGDLGVRKGLQVLYGLKELPGALKME 243
D + L G+G M+FS+ K PV D V+K + LY ++ +
Sbjct: 206 DNECHEELKKFMGVGPQVADCIMLFSMQKYSAFPV-DTWVKKAMMSLYVAPDVSLKKIRD 264
Query: 244 EVCEKWKPYRSVGSWYMWRL 263
EK+ Y++
Sbjct: 265 FGREKFGSLSGFAQQYLFYY 284
>2xhi_A N-glycosylase/DNA lyase; lyase-DNA complex, lyase/DNA complex,
separation-OF-function helix-hairpin-helix, DNA repair;
HET: 8OG; 1.55A {Homo sapiens} PDB: 1ko9_A 1lwy_A*
1hu0_A* 1lwv_A* 1lww_A* 2noe_A* 2noh_A* 2nol_A* 1n3c_A*
1fn7_A* 2noz_A* 1yqk_A 1yqr_A* 1yql_A* 1yqm_A* 2noi_A
1ebm_A* 1m3q_A* 1m3h_A* 1n39_A* ...
Length = 360
Score = 109 bits (274), Expect = 4e-28
Identities = 33/217 (15%), Positives = 54/217 (24%), Gaps = 27/217 (12%)
Query: 70 DIALRHLRDKDPLLATLIDAHRPPTFESSRSPFLSLAKSILYQQLAYKAAKSIYTRFVAL 129
H D + + P L I + R
Sbjct: 122 AQLYHHWGSVDSHFQEVAQKFQGVRLLRQ-DPIECLFSFICSSNNNIARITGMVERLCQA 180
Query: 130 FNGEDNIL----------PDAVLAVSP-QQLREIGVSYRKASYLRDLAEKYTDGILSD-- 176
F L A+ LR++G+ YR A Y+ A +
Sbjct: 181 FGPRLIQLDDVTYHGFPSLQALAGPEVEAHLRKLGLGYR-ARYVSASARAILEEQGGLAW 239
Query: 177 -ESIVEMDDVTMFKMLTSVKGIGAWSVHMFMIFSLHKPDVLPVGDLGVRKGLQVLYGLKE 235
+ + E K L + G+G + +L KP +PV ++ + Q Y
Sbjct: 240 LQQLRESSYEEAHKALCILPGVGTCVADKICLMALDKPQAVPV-NVHMWHIAQRDYSWHP 298
Query: 236 LPGALKM----------EEVCEKWKPYRSVGSWYMWR 262
K W PY ++
Sbjct: 299 TTSQAKGPSPQTNKELGNFFRSLWGPYAGWAQAVLFS 335
>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 = 54.3 bits (130), Expect = 2e-08
Identities = 47/249 (18%), Positives = 82/249 (32%), Gaps = 79/249 (31%)
Query: 71 IALRH-----LRDKDP--LLATLIDAHRPPTFES-------------SRSPFLSLAKSIL 110
+ L L D L A L+ + ++ ++ PF + S L
Sbjct: 86 LCLTEFENCYLEGNDIHALAAKLLQENDTTLVKTKELIKNYITARIMAKRPFDKKSNSAL 145
Query: 111 YQQLAYKAAKSIYTRFVALFNGEDNILPDAVLAVSPQQLREIGVSYRKASYLRDLAEKYT 170
++ A + VA+F G+ N D ++LR++ +Y + DL + +
Sbjct: 146 FR-----AVGEGNAQLVAIFGGQGNT--DDYF----EELRDLYQTYH--VLVGDLIKF-S 191
Query: 171 DGILSDESIVEMDDVTMFKMLTSVKG--IGAWSVHMFMIFSLHKPDVLPVGD-------- 220
LS+ +D +F +G I W L P P D
Sbjct: 192 AETLSELIRTTLDAEKVFT-----QGLNILEW---------LENPSNTPDKDYLLSIPIS 237
Query: 221 ---LGVRKGLQVLYGLKEL---PGALKMEEVCEKWKPYRSVGSWYMWRLMEAKGVLPNVA 274
+GV + + K L PG L+ G+ ++G++ VA
Sbjct: 238 CPLIGVIQLAHYVVTAKLLGFTPGELRS----------YLKGA-----TGHSQGLVTAVA 282
Query: 275 KAAVTSVEA 283
A S E+
Sbjct: 283 IAETDSWES 291
Score = 53.9 bits (129), Expect = 3e-08
Identities = 39/206 (18%), Positives = 61/206 (29%), Gaps = 82/206 (39%)
Query: 9 DNISQNPS----ASSKITFP--------------------PRKIRK-LTTITPITKIAEI 43
+N S P S I+ P P ++R L T +
Sbjct: 220 ENPSNTPDKDYLLSIPISCPLIGVIQLAHYVVTAKLLGFTPGELRSYLKGAT--GHSQGL 277
Query: 44 PVATAISTNS------DNSPKIFKPLTFKGEVDIALRHLRDKDPLLATLIDAHR------ 91
A AI+ + K L F I +R +
Sbjct: 278 VTAVAIAETDSWESFFVSVRKAITVLFF-----IGVR--------------CYEAYPNTS 318
Query: 92 -PPTF--------ESSRSPFLS---LAKSILYQQLAY-----KAAKSIYTRFVALFNGED 134
PP+ E SP LS L + + + A K + ++L NG
Sbjct: 319 LPPSILEDSLENNEGVPSPMLSISNLTQEQVQDYVNKTNSHLPAGKQVE---ISLVNGAK 375
Query: 135 NILPDAVLAVSPQQLREIGVSYRKAS 160
N+ V++ PQ L + ++ RKA
Sbjct: 376 NL----VVSGPPQSLYGLNLTLRKAK 397
Score = 43.1 bits (101), Expect = 7e-05
Identities = 44/255 (17%), Positives = 72/255 (28%), Gaps = 97/255 (38%)
Query: 28 IRKLTTITPITKIAEI----PVATAISTNSDNSPKIF----KPLTFKGEVDIALRHLRDK 79
I LT + + P + + N K P + G +++ LR +
Sbjct: 341 ISNLTQEQVQDYVNKTNSHLPAGKQVEISLVNGAKNLVVSGPPQSLYG-LNLTLRKAK-- 397
Query: 80 DPLLATLIDAHRPPTFESSRSPFLSLAKSILYQQLAYKAAKSIYTRFV---ALFNGEDNI 136
P + SR PF S + RF+ + F+ +
Sbjct: 398 -----------APSGLDQSRIPF-S------------ERKLKFSNRFLPVASPFHSH--L 431
Query: 137 LPDAVLAVSPQQLREIGVSYRKASYLR----------DLAEKYTDGILSDESIVEM---- 182
L A + + L + VS+ A ++ DL + I E IV+
Sbjct: 432 LVPASDLI-NKDLVKNNVSF-NAKDIQIPVYDTFDGSDLRV-LSGSIS--ERIVDCIIRL 486
Query: 183 ----DDVTMFK----------------MLTS--VKGIGAWSVHMFMIFSLHKPDVLPVGD 220
+ T FK +LT G G V+ G
Sbjct: 487 PVKWETTTQFKATHILDFGPGGASGLGVLTHRNKDGTGV--------------RVIVAGT 532
Query: 221 LGVRKGLQVLYGLKE 235
L + YG K+
Sbjct: 533 LDI--NPDDDYGFKQ 545
Score = 34.6 bits (79), Expect = 0.034
Identities = 36/202 (17%), Positives = 60/202 (29%), Gaps = 81/202 (40%)
Query: 110 LYQQLAYKAAKSIYTR----------FVALFNGEDNILPDAVLAV--SPQQLREIGVSYR 157
LY+ KAA+ ++ R F L +N P L + ++ + I +Y
Sbjct: 1635 LYK--TSKAAQDVWNRADNHFKDTYGFSILDIVINN--PVN-LTIHFGGEKGKRIRENYS 1689
Query: 158 KASYLRDLAEKYTDGILSDESIVEMDDVTMFKMLTSVKGIGAWSVHMFMIFSLHKPDVLP 217
+ E DG L E I + + TS F
Sbjct: 1690 AMIF-----ETIVDGKLKTEKIFKEINEH----STSY------------TFR-S-----E 1722
Query: 218 VGDLGVRKGLQVLYGLKELPGALKMEEVCEKWKPYRSVGSWYMWRLMEAKGVLPN----- 272
G L + Q P AL + E + +++KG++P
Sbjct: 1723 KGLLSATQFTQ--------P-ALTLMEKA-------------AFEDLKSKGLIPADATFA 1760
Query: 273 ----------VAKAAVTSVEAA 284
+ A V S+E+
Sbjct: 1761 GHSLGEYAALASLADVMSIESL 1782
Score = 30.0 bits (67), Expect = 1.1
Identities = 20/86 (23%), Positives = 32/86 (37%), Gaps = 23/86 (26%)
Query: 19 SKITFPPRKIRKLTTITPIT-------------KIAEIPVATAISTNSDNSPKIFKPL-- 63
S+I F RK++ P+ I + V +S N+ +I P+
Sbjct: 405 SRIPFSERKLKFSNRFLPVASPFHSHLLVPASDLINKDLVKNNVSFNA-KDIQI--PVYD 461
Query: 64 TFKGEVDIALRHLRDKDPLLATLIDA 89
TF G D LR L + ++D
Sbjct: 462 TFDGS-D--LRVL--SGSISERIVDC 482
>1pu6_A 3-methyladenine DNA glycosylase; helix-hairpin-helix, base excision
repair, hydrolase; HET: KCX; 1.64A {Helicobacter pylori}
SCOP: a.96.1.5 PDB: 1pu7_A* 1pu8_A*
Length = 218
Score = 42.8 bits (101), Expect = 4e-05
Identities = 28/145 (19%), Positives = 53/145 (36%), Gaps = 14/145 (9%)
Query: 82 LLATLIDAHRPPTFESSRSPFLSLAKSILYQQ----LAYKAAKSIYTRFVALFNGEDNIL 137
L + + + P + + F +L ++L Q K+ +++ F+ + E N
Sbjct: 11 LKSLDLLKNAPAWWWPNALKFEALLGAVLTQNTKFEAVLKSLENLKNAFILENDDEIN-- 68
Query: 138 PDAVLAVSPQQL----REIGVSYRKASYLRDLAEKYTDGILSDESIVEMDDVTMFKMLTS 193
+ + +L R G +KA L DL+ +S + L
Sbjct: 69 LKKIAYIEFSKLAECVRPSGFYNQKAKRLIDLSGNILKDF---QSFENFKQEVTREWLLD 125
Query: 194 VKGIGAWSVHMFMIFSLHKPDVLPV 218
KGIG S + ++ K V+ V
Sbjct: 126 QKGIGKESADAILCYACAKE-VMVV 149
>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 = 36.8 bits (84), Expect = 0.008
Identities = 43/301 (14%), Positives = 90/301 (29%), Gaps = 107/301 (35%)
Query: 38 TKIAEIPVATAISTNS--------DNSPKIFKPLTFKGEVDI-----ALRHLRDKDPL-- 82
+ I ++ T N ++F AL LR +
Sbjct: 96 SPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLI 155
Query: 83 ----------LATLIDAHRPPTFESSRSPF----LSLAK-----SIL--YQQLAYKAAKS 121
+A +D + + F L+L ++L Q+L Y+ +
Sbjct: 156 DGVLGSGKTWVA--LDVCLSYKVQC-KMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPN 212
Query: 122 IYTRFVALFNGEDNILPDAVLAVSPQQLREIGVSYRKASYLRDL--AEKYTDGILSDESI 179
+ + + NI ++ I + LR L ++ Y + +L +
Sbjct: 213 ----WTSRSDHSSNI---------KLRIHSI------QAELRRLLKSKPYENCLL----V 249
Query: 180 VEMDDV------TMF----KML--TSVKGI-----GAWSVHMFMIFSLHKPDVLPVGDLG 222
+ +V F K+L T K + A + H+ + H L ++
Sbjct: 250 --LLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLD---HHSMTLTPDEV- 303
Query: 223 VRKGLQVLY---GLKELP--------------GALKMEEVCEKWKPYRSVGSWYMWRLME 265
K L + Y ++LP + + W ++ V + ++E
Sbjct: 304 --KSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLA-TWDNWKHVNCDKLTTIIE 360
Query: 266 A 266
+
Sbjct: 361 S 361
Score = 36.0 bits (82), Expect = 0.013
Identities = 36/186 (19%), Positives = 57/186 (30%), Gaps = 50/186 (26%)
Query: 54 DN--SPKIFKPLTFKGEVDIALRHL---RDKDPLLATLIDAHRPPTFESSRSPF-LSLAK 107
N + K + F +++ + L R K + + K
Sbjct: 251 LNVQNAKAWN--AF----NLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVK 304
Query: 108 SILYQQLAYKAAKSIYTRFVALFNGEDNILPDAVLAVSPQQLREIGVSYRKAS-----YL 162
S+L K + R +D LP VL +P++L I S R +
Sbjct: 305 SLL--------LKYLDCRP------QD--LPREVLTTNPRRLSIIAESIRDGLATWDNWK 348
Query: 163 RDLAEKYTDGI-LSDESIVEMDDVTMFKMLT----SVKGIGA------W-----SVHMFM 206
+K T I S + + MF L+ S I W S M +
Sbjct: 349 HVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAH-IPTILLSLIWFDVIKSDVMVV 407
Query: 207 IFSLHK 212
+ LHK
Sbjct: 408 VNKLHK 413
Score = 30.6 bits (68), Expect = 0.72
Identities = 20/107 (18%), Positives = 36/107 (33%), Gaps = 28/107 (26%)
Query: 23 FPPRKIRKLTTITPITKIAEIPVATAISTNSDNSPKIFKPLTFKGEVDIALRHLRDKDPL 82
F +KIR A + ++T K +K ++ D DP
Sbjct: 502 FLEQKIRH-------DSTAWNASGSILNTLQQ--LKFYK------------PYICDNDPK 540
Query: 83 LATLIDA--HRPPTFESS--RSPFLSLAKSILYQQ---LAYKAAKSI 122
L++A P E + S + L + L + + +A K +
Sbjct: 541 YERLVNAILDFLPKIEENLICSKYTDLLRIALMAEDEAIFEEAHKQV 587
Score = 30.6 bits (68), Expect = 0.78
Identities = 13/85 (15%), Positives = 23/85 (27%), Gaps = 8/85 (9%)
Query: 203 HMFMIFS-----LHKPDVLPVGDLGVRKGLQVLYGLKELPGALKMEEVCEKWK-PYRSVG 256
H M F D+L V + L EE+ G
Sbjct: 4 HHHMDFETGEHQYQYKDILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSG 63
Query: 257 SWYMWRLMEAKGVLPNVAKAAVTSV 281
+ ++ + +K + + V V
Sbjct: 64 TLRLFWTLLSKQ--EEMVQKFVEEV 86
>1l0w_A Aspartyl-tRNA synthetase; space-grown crystal, dimeric enzyme,
flexible domains, ligase; 2.01A {Thermus thermophilus}
SCOP: b.40.4.1 d.74.4.1 d.104.1.1 PDB: 1efw_A* 1g51_A
Length = 580
Score = 32.9 bits (76), Expect = 0.11
Identities = 13/49 (26%), Positives = 19/49 (38%), Gaps = 15/49 (30%)
Query: 125 RFVALFNGEDNI---------------LPDAVLAVSPQQLREIGVSYRK 158
R +AL G +I L A V +QLRE+G+ +
Sbjct: 531 RLLALMTGSPSIREVIAFPKNKEGKDPLTGAPSPVPEEQLRELGLMVVR 579
>1c0a_A Aspartyl tRNA synthetase; protein-RNA complex, ligase/RNA complex;
HET: 4SU H2U QUO G7M 5MU PSU AMP AMO; 2.40A {Escherichia
coli} SCOP: b.40.4.1 d.74.4.1 d.104.1.1 PDB: 1il2_A*
1eqr_A*
Length = 585
Score = 32.8 bits (76), Expect = 0.11
Identities = 11/49 (22%), Positives = 16/49 (32%), Gaps = 15/49 (30%)
Query: 125 RFVALFNGEDNI---------------LPDAVLAVSPQQLREIGVSYRK 158
R L G DNI + +A +P L E+ + K
Sbjct: 537 RLTMLLTGTDNIRDVIAFPKTTAAACLMTEAPSFANPTALAELSIQVVK 585
>4e9f_A Methyl-CPG-binding domain protein 4; HHH DNA glycosylase family,
hydrolase-DNA complex; HET: DNA 3DR; 1.79A {Homo
sapiens} PDB: 4e9e_A* 4e9g_A* 4e9h_A* 4ea5_A* 4dk9_A*
1ngn_A 4ea4_A* 4ew4_A* 4evv_A* 4ew0_A* 3iho_A
Length = 161
Score = 29.8 bits (67), Expect = 0.57
Identities = 24/144 (16%), Positives = 52/144 (36%), Gaps = 27/144 (18%)
Query: 98 SRSPFLSLAKSILYQQLAYKAAKSIYTRFVALFNGEDNILPDA-VLAVSPQQ-----LRE 151
P+ L +I + + K A + +F+ + P A V + + L+
Sbjct: 28 FHDPWKLLIATIFLNRTSGKMAIPVLWKFLEKY-------PSAEVARTADWRDVSELLKP 80
Query: 152 IGVSYRKASYLRDLAEKYTDGILSDESIVEMDDVTMFKMLTSVKGIGAWSVHMFMIFSLH 211
+G+ +A + + D L+ + +K + GIG + + IF ++
Sbjct: 81 LGLYDLRAKTIVKFS----DEYLTKQ----------WKYPIELHGIGKYGNDSYRIFCVN 126
Query: 212 KPDVLPVGDLGVRKGLQVLYGLKE 235
+ + D + K L+ E
Sbjct: 127 EWKQVHPEDHKLNKYHDWLWENHE 150
>3d31_A Sulfate/molybdate ABC transporter, ATP-binding protein;
ATP-binding, nucleotide-binding, membrane,
transmembrane, transport protein; 3.00A {Methanosarcina
acetivorans} SCOP: b.40.6.3 c.37.1.12
Length = 348
Score = 28.7 bits (65), Expect = 2.1
Identities = 11/43 (25%), Positives = 18/43 (41%), Gaps = 6/43 (13%)
Query: 112 QQLAYKAAKSIY----TRFVALFNGEDNILPDAVLAVSPQQLR 150
Q+ + I+ VA F G +N+L V++ LR
Sbjct: 207 IQVG--KPEEIFEKPVEGRVASFVGFENVLKGRVISAEQGLLR 247
>2onk_A Molybdate/tungstate ABC transporter, ATP-binding protein; membrane
protein; 3.10A {Archaeoglobus fulgidus} SCOP: c.37.1.12
Length = 240
Score = 27.9 bits (63), Expect = 3.3
Identities = 5/26 (19%), Positives = 9/26 (34%), Gaps = 3/26 (11%)
Query: 122 IY---TRFVALFNGEDNILPDAVLAV 144
++ VA F N+L +
Sbjct: 214 LFSAKNGEVAEFLSARNLLLKVSKIL 239
>4eqm_A Protein kinase; transferase; HET: ANP; 3.00A {Staphylococcus aureus
subsp}
Length = 294
Score = 28.0 bits (63), Expect = 3.6
Identities = 11/35 (31%), Positives = 19/35 (54%), Gaps = 2/35 (5%)
Query: 65 FKGE--VDIALRHLRDKDPLLATLIDAHRPPTFES 97
F GE V IA++H++D P + T + P + +
Sbjct: 212 FNGETAVSIAIKHIQDSVPNVTTDVRKDIPQSLSN 246
>3fvq_A Fe(3+) IONS import ATP-binding protein FBPC; nucleotide binding
domain, ABC motor domain, ferric iron transport, cell
inner membrane; HET: ATP; 1.90A {Neisseria gonorrhoeae}
Length = 359
Score = 27.9 bits (63), Expect = 3.6
Identities = 11/36 (30%), Positives = 15/36 (41%), Gaps = 6/36 (16%)
Query: 112 QQLAYKAAKSIY----TRFVALFNGEDNILPDAVLA 143
Q A + +Y ALF GE + P A+ A
Sbjct: 218 LQTA--SPHELYRQPADLDAALFIGEGIVFPAALNA 251
>1vr3_A Acireductone dioxygenase; 13543033, structural genomics, JOI for
structural genomics, JCSG, protein structure initiative
oxidoreductase; 2.06A {Mus musculus} SCOP: b.82.1.6
Length = 191
Score = 27.3 bits (60), Expect = 4.2
Identities = 13/45 (28%), Positives = 21/45 (46%)
Query: 143 AVSPQQLREIGVSYRKASYLRDLAEKYTDGILSDESIVEMDDVTM 187
VS +QLR +GV Y K + + + I + MD +T+
Sbjct: 37 PVSLEQLRTLGVLYWKLDADKYENDPELEKIRKMRNYSWMDIITI 81
>1wzz_A Probable endoglucanase; glycoside hydrolase family 8 (GH-8),
(alpha/alpha)6 barrel, structural genomics; 1.65A
{Gluconacetobacter xylinus} SCOP: a.102.1.2
Length = 334
Score = 27.3 bits (60), Expect = 6.7
Identities = 10/62 (16%), Positives = 17/62 (27%), Gaps = 1/62 (1%)
Query: 111 YQQLAYKAAKSIYTRFVALFNGEDNILPDAVLAVSPQQLREIGVSYRKASYLRDLAEKYT 170
Y Q A + ++P AV + + +SY L +
Sbjct: 127 YIQDAMAIYGDVLNLMTMKAGPYVVLMPGAVGFTKKDSVI-LNLSYYVMPSLLQAFDLTA 185
Query: 171 DG 172
D
Sbjct: 186 DP 187
>1z47_A CYSA, putative ABC-transporter ATP-binding protein; alpha/beta
motif, beta sandwich, ligand binding protein; 1.90A
{Alicyclobacillus acidocaldarius}
Length = 355
Score = 27.2 bits (61), Expect = 6.8
Identities = 9/21 (42%), Positives = 11/21 (52%), Gaps = 4/21 (19%)
Query: 122 IY----TRFVALFNGEDNILP 138
+Y T FVA F GE N+
Sbjct: 233 VYEKPGTLFVASFIGESNVWT 253
>3oo3_A OXY protein; cytochrome P450, monooxygenase, PCD-teicoplanin
aglycone, oxidoreductase; HET: HEM; 2.20A {Actinoplanes
teichomyceticus} PDB: 3o1a_A*
Length = 384
Score = 26.8 bits (60), Expect = 8.6
Identities = 7/21 (33%), Positives = 11/21 (52%)
Query: 217 PVGDLGVRKGLQVLYGLKELP 237
P DL + G + ++ELP
Sbjct: 361 PEEDLRFKPGRPAPFAVEELP 381
>1y8a_A Hypothetical protein AF1437; structural genomics, protein structu
initiative, PSI, midwest center for structural genomics;
1.40A {Archaeoglobus fulgidus} SCOP: c.108.1.24
Length = 332
Score = 26.7 bits (58), Expect = 8.9
Identities = 15/74 (20%), Positives = 33/74 (44%), Gaps = 5/74 (6%)
Query: 129 LFNGEDNILPDAVLAVSPQQLREIGVSYRKASYLRDLAEKYTDGILSDESIVEMDDVTMF 188
LF D + + + + ++ +G + KA +R E D +V D ++ +
Sbjct: 180 LFRKLDELFSRSEVRKIVESVKAVG-AGEKAKIMRGYCESKG----IDFPVVVGDSISDY 234
Query: 189 KMLTSVKGIGAWSV 202
KM + +G+G ++
Sbjct: 235 KMFEAARGLGGVAI 248
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 0.133 0.386
Gapped
Lambda K H
0.267 0.0771 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 4,297,063
Number of extensions: 254123
Number of successful extensions: 621
Number of sequences better than 10.0: 1
Number of HSP's gapped: 593
Number of HSP's successfully gapped: 39
Length of query: 284
Length of database: 6,701,793
Length adjustment: 93
Effective length of query: 191
Effective length of database: 4,105,140
Effective search space: 784081740
Effective search space used: 784081740
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 (25.7 bits)