RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy9547
(363 letters)
>3fsp_A A/G-specific adenine glycosylase; protein-DNA complex, DNA
glycosylase, transition state analog, DNA repair; HET:
NRI; 2.20A {Geobacillus stearothermophilus} PDB: 3fsq_A*
1rrs_A* 1vrl_A* 1rrq_A* 3g0q_A*
Length = 369
Score = 461 bits (1189), Expect = e-164
Identities = 153/362 (42%), Positives = 218/362 (60%), Gaps = 4/362 (1%)
Query: 1 MASNLSAKEILAFQESILTWYKQNARQLPWRESNNPYYVWISEVMLQQTQVKTVLPYYEK 60
M FQ +L W+ + R LPWR+ +PY VW+SEVMLQQT+V+TV+PY+E+
Sbjct: 4 MTRETERFPAREFQRDLLDWFARERRDLPWRKDRDPYKVWVSEVMLQQTRVETVIPYFEQ 63
Query: 61 FIKTYPTIKDFAFDTEDNVLKMWEGLGYYSRVRNFQAGCRQVIEQFGGEVPRDKKQLLSI 120
FI +PT++ A ED VLK WEGLGYYSRVRN A ++V ++GG+VP D + +
Sbjct: 64 FIDRFPTLEALADADEDEVLKAWEGLGYYSRVRNLHAAVKEVKTRYGGKVPDDPDEFSRL 123
Query: 121 KGVGDYTAGALASICYNIPTPAVDGNVFRIYGRLFEIEDDISKGKTKVVYETLVSKTMSQ 180
KGVG YT GA+ S+ Y +P PAVDGNV R+ RLF + DDI+K T+ +E +V + M+
Sbjct: 124 KGVGPYTVGAVLSLAYGVPEPAVDGNVMRVLSRLFLVTDDIAKPSTRKRFEQIVREIMAY 183
Query: 181 TNAREFNQALMDLGATVCLFKNPKCKECPLSRFCSAYKNNTIENFPVKLGKTKVKDVFLL 240
N FN+AL++LGA VC + P C CP+ +C A+ E PVK+ KT VK V L
Sbjct: 184 ENPGAFNEALIELGALVCTPRRPSCLLCPVQAYCQAFAEGVAEELPVKMKKTAVKQVPLA 243
Query: 241 TVVVKTDTNKYLIQKRPTTGLLSNFYMFLSFESDTPYTSQ--VEFLSENLPFKVNLNEKC 298
V+ D + LI+KR +TGLL+N + F S E+D + + + E +V L E
Sbjct: 244 VAVLADDEGRVLIRKRDSTGLLANLWEFPSCETDGADGKEKLEQMVGEQYGLQVELTEP- 302
Query: 299 LGNVKHVFSHLKWNMDVYSGTAKEKTIPANKTYKLITETQMKKYAFPVPYQKVWKLFTKS 358
+ + +H FSHL W + V+ G P + Y+L E ++K YAFPV +Q+VW+ + +
Sbjct: 303 IVSFEHAFSHLVWQLTVFPGRLVHGG-PVEEPYRLAPEDELKAYAFPVSHQRVWREYKEW 361
Query: 359 KG 360
Sbjct: 362 AS 363
>3n5n_X A/G-specific adenine DNA glycosylase; alpha-helices,
helix-hairpin-helix motif, iron-sulfur cluste hydrolase;
2.30A {Homo sapiens}
Length = 287
Score = 363 bits (933), Expect = e-126
Identities = 99/272 (36%), Positives = 135/272 (49%), Gaps = 11/272 (4%)
Query: 6 SAKEILAFQESILTWYKQNARQLPWRESN--------NPYYVWISEVMLQQTQVKTVLPY 57
E+ AF+ S+L+WY Q R LPWR Y VW+SEVMLQQTQV TV+ Y
Sbjct: 11 DVAEVTAFRGSLLSWYDQEKRDLPWRRRAEDEMDLDRRAYAVWVSEVMLQQTQVATVINY 70
Query: 58 YEKFIKTYPTIKDFAFDTEDNVLKMWEGLGYYSRVRNFQAGCRQVIEQFGGEVPRDKKQL 117
Y +++ +PT++D A + + V ++W GLGYYSR R Q G R+V+E+ GG +PR + L
Sbjct: 71 YTGWMQKWPTLQDLASASLEEVNQLWAGLGYYSRGRRLQEGARKVVEELGGHMPRTAETL 130
Query: 118 LS-IKGVGDYTAGALASICYNIPTPAVDGNVFRIYGRLFEIEDDISKGKTKVVYETLVSK 176
+ GVG YTAGA+ASI + T VDGNV R+ R+ I D S L +
Sbjct: 131 QQLLPGVGRYTAGAIASIAFGQATGVVDGNVARVLCRVRAIGADPSSTLVSQQLWGLAQQ 190
Query: 177 TMSQTNAREFNQALMDLGATVCLFKNPKCKECPLSRFCSAYKNNTIENFPVKLGKTKVKD 236
+ +FNQA M+LGATVC + P C +CP+ C A + E + D
Sbjct: 191 LVDPARPGDFNQAAMELGATVCTPQRPLCSQCPVESLCRARQRVEQEQLLASGSLSGSPD 250
Query: 237 VFLLTVVVKTDTNKYLIQKRPTTGLLSNFYMF 268
V T + F
Sbjct: 251 V--EECAPNTGQCHLCLPPSEPWDQTLGVVNF 280
>1kg2_A A/G-specific adenine glycosylase; DNA repair, hydrolase; 1.20A
{Escherichia coli} SCOP: a.96.1.2 PDB: 1kg3_A 1muy_A
1kg6_A 1kg5_A 1mun_A 1mud_A 1kg4_A 1weg_A 1wei_A*
1wef_A* 1kg7_A 1kqj_A
Length = 225
Score = 355 bits (914), Expect = e-124
Identities = 89/221 (40%), Positives = 123/221 (55%), Gaps = 1/221 (0%)
Query: 12 AFQESILTWYKQNARQ-LPWRESNNPYYVWISEVMLQQTQVKTVLPYYEKFIKTYPTIKD 70
F +L WY + R+ LPW+ PY VW+SEVMLQQTQV TV+PY+E+F+ +PT+ D
Sbjct: 5 QFSAQVLDWYDKYGRKTLPWQIDKTPYKVWLSEVMLQQTQVATVIPYFERFMARFPTVTD 64
Query: 71 FAFDTEDNVLKMWEGLGYYSRVRNFQAGCRQVIEQFGGEVPRDKKQLLSIKGVGDYTAGA 130
A D VL +W GLGYY+R RN +QV GG+ P +++ ++ GVG TAGA
Sbjct: 65 LANAPLDEVLHLWTGLGYYARARNLHKAAQQVATLHGGKFPETFEEVAALPGVGRSTAGA 124
Query: 131 LASICYNIPTPAVDGNVFRIYGRLFEIEDDISKGKTKVVYETLVSKTMSQTNAREFNQAL 190
+ S+ P +DGNV R+ R + + K + + +L + FNQA+
Sbjct: 125 ILSLSLGKHFPILDGNVKRVLARCYAVSGWPGKKEVENKLWSLSEQVTPAVGVERFNQAM 184
Query: 191 MDLGATVCLFKNPKCKECPLSRFCSAYKNNTIENFPVKLGK 231
MDLGA +C PKC CPL C A NN+ +P K K
Sbjct: 185 MDLGAMICTRSKPKCSLCPLQNGCIAAANNSWALYPGKKPK 225
>1kea_A Possible G-T mismatches repair enzyme; DNA repair, DNA glycosylase,
DNA mismatch, methylation; 2.00A {Methanothermobacter
thermautotrophicusorganism_taxid} SCOP: a.96.1.2
Length = 221
Score = 348 bits (896), Expect = e-121
Identities = 65/220 (29%), Positives = 110/220 (50%), Gaps = 2/220 (0%)
Query: 3 SNLSAKEILAFQESILTWYKQNARQLPWRESNNPYYVWISEVMLQQTQVKTVLPYYEKFI 62
+ + K+ F +ILT++ + R PWR + +PY + I+E++L++T V Y+KF
Sbjct: 2 DDATNKKRKVFVSTILTFWNTDRRDFPWRHTRDPYVILITEILLRRTTAGHVKKIYDKFF 61
Query: 63 KTYPTIKDFAFDTEDNVLKMWEGLGYYS-RVRNFQAGCRQVIEQFGGEVPRDKKQLLSIK 121
Y +D + + K + +G + R + R VI +GG VPR++K +L +
Sbjct: 62 VKYKCFEDILKTPKSEIAKDIKEIGLSNQRAEQLKELARVVINDYGGRVPRNRKAILDLP 121
Query: 122 GVGDYTAGALASICYNIPTPAVDGNVFRIYGRLFEIEDDISKGKTKVVYETLVSKTMSQT 181
GVG YT A+ + + VD N R+ R F + K ++E L +
Sbjct: 122 GVGKYTCAAVMCLAFGKKAAMVDANFVRVINRYFGGSYENLNYNHKALWE-LAETLVPGG 180
Query: 182 NAREFNQALMDLGATVCLFKNPKCKECPLSRFCSAYKNNT 221
R+FN LMD A +C + PKC++C +S+ CS Y+ +
Sbjct: 181 KCRDFNLGLMDFSAIICAPRKPKCEKCGMSKLCSYYEKCS 220
>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 = 142 bits (359), Expect = 1e-41
Identities = 25/140 (17%), Positives = 59/140 (42%), Gaps = 8/140 (5%)
Query: 28 LPWRESNNPYYVWISEVMLQQTQVKTVLPYYEKFIKTYPTIKDFAFDTEDNVLKMWEGLG 87
+ ++P+ + I+ + L +T K +P KF++ YP+ + +V ++ + LG
Sbjct: 23 VQETLFHDPWKLLIATIFLNRTSGKMAIPVLWKFLEKYPSAEVARTADWRDVSELLKPLG 82
Query: 88 YYSRVRNFQAGCRQVIEQFGGEVPRDKKQLLSIKGVGDYTAGALASICYN--IPTPAVDG 145
Y +R + +++ + + K + + G+G Y + C N D
Sbjct: 83 LY-DLR-----AKTIVKFSDEYLTKQWKYPIELHGIGKYGNDSYRIFCVNEWKQVHPEDH 136
Query: 146 NVFRIYGRLFEIEDDISKGK 165
+ + + L+E + +S
Sbjct: 137 KLNKYHDWLWENHEKLSLSH 156
>1x51_A A/G-specific adenine DNA glycosylase; nudix domain, DNA repair,
alpha-3 isoform, structural genomics, NPPSFA; NMR {Homo
sapiens} SCOP: d.113.1.3
Length = 155
Score = 106 bits (267), Expect = 4e-28
Identities = 28/149 (18%), Positives = 57/149 (38%), Gaps = 9/149 (6%)
Query: 221 TIENFPVKLGKTKVKDVFLLTVVVK---TDTNKYLIQKRPTTGLLSNFYMFLSFE----S 273
+ + P K + ++ T V++ + L+ +RP +GLL+ + F S
Sbjct: 3 SGSSGPRKASRKPPREESSATCVLEQPGALGAQILLVQRPNSGLLAGLWEFPSVTWEPSE 62
Query: 274 DTPYTSQVEFLSENLPFKVNLNEKCLGNVKHVFSHLKWNMDVYSG--TAKEKTIPANKTY 331
+ ++ L + + LG V H FSH+K VY +
Sbjct: 63 QLQRKALLQELQRWAGPLPATHLRHLGEVVHTFSHIKLTYQVYGLALEGQTPVTTVPPGA 122
Query: 332 KLITETQMKKYAFPVPYQKVWKLFTKSKG 360
+ +T+ + A +KV++++ G
Sbjct: 123 RWLTQEEFHTAAVSTAMKKVFRVYQGQSG 151
>2abk_A Endonuclease III; DNA-repair, DNA glycosylase; 1.85A {Escherichia
coli} SCOP: a.96.1.1
Length = 211
Score = 85.7 bits (213), Expect = 7e-20
Identities = 41/161 (25%), Positives = 67/161 (41%), Gaps = 6/161 (3%)
Query: 63 KTYPTIKDFAFDTEDNVLKMWEGLGYY-SRVRNFQAGCRQVIEQFGGEVPRDKKQLLSIK 121
T + V + +G Y S+ N CR ++EQ GEVP D+ L ++
Sbjct: 56 PVANTPAAMLELGVEGVKTYIKTIGLYNSKAENIIKTCRILLEQHNGEVPEDRAALEALP 115
Query: 122 GVGDYTAGALASICYNIPTPAVDGNVFRIYGRLFEIEDDISKGKTKVVYETLVSKTMSQT 181
GVG TA + + + PT AVD ++FR+ R + GK E + K +
Sbjct: 116 GVGRKTANVVLNTAFGWPTIAVDTHIFRVCNRT-----QFAPGKNVEQVEEKLLKVVPAE 170
Query: 182 NAREFNQALMDLGATVCLFKNPKCKECPLSRFCSAYKNNTI 222
+ + L+ G C+ + P+C C + C + I
Sbjct: 171 FKVDCHHWLILHGRYTCIARKPRCGSCIIEDLCEYKEKVDI 211
>1orn_A Endonuclease III; DNA repair, DNA glycosylase, [4Fe-4S] cluster,
iron-sulfur cluster, hydrolase/DNA complex; HET: PED;
1.70A {Geobacillus stearothermophilus} SCOP: a.96.1.1
PDB: 1orp_A* 1p59_A*
Length = 226
Score = 85.0 bits (211), Expect = 2e-19
Identities = 42/171 (24%), Positives = 78/171 (45%), Gaps = 7/171 (4%)
Query: 63 KTYPTIKDFAFDTEDNVLKMWEGLGYY-SRVRNFQAGCRQVIEQFGGEVPRDKKQLLSIK 121
+ Y T D+ + + + +G Y ++ RN Q C +I+++ GEVPRD+ +L+ +
Sbjct: 60 EKYRTPHDYIAVPLEELEQDIRSIGLYRNKARNIQKLCAMLIDKYNGEVPRDRDELMKLP 119
Query: 122 GVGDYTAGALASICYNIPTPAVDGNVFRIYGRLFEIEDDISK-GKTKVVYETLVSKTMSQ 180
GVG TA + S+ + +P AVD +V R+ RL + + + E + K + +
Sbjct: 120 GVGRKTANVVVSVAFGVPAIAVDTHVERVSKRL-----GFCRWDDSVLEVEKTLMKIIPK 174
Query: 181 TNAREFNQALMDLGATVCLFKNPKCKECPLSRFCSAYKNNTIENFPVKLGK 231
+ ++ G C ++P+C CPL C K + +
Sbjct: 175 EEWSITHHRMIFFGRYHCKAQSPQCPSCPLLHLCREGKKRMRKREEKAANQ 225
>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 = 77.5 bits (191), Expect = 8e-17
Identities = 32/217 (14%), Positives = 74/217 (34%), Gaps = 27/217 (12%)
Query: 5 LSAKEILAFQESILTWYKQNARQLPWRESNNPYYVWISEVMLQQTQVKTVLPYYEKFIKT 64
L + EIL +++ + W + + + V+ Q T+ + VL E
Sbjct: 2 LDSFEIL---KALKSLDLLKNAPAWWWPNALKFEALLGAVLTQNTKFEAVLKSLENLKNA 58
Query: 65 YPTIKDFAFDTEDNVLKM-WEGL-------GYY-SRVRNFQAGCRQVIEQFGG----EVP 111
+ D + + + + + L G+Y + + +++ F +
Sbjct: 59 FILENDDEINLKK-IAYIEFSKLAECVRPSGFYNQKAKRLIDLSGNILKDFQSFENFKQE 117
Query: 112 RDKKQLLSIKGVGDYTAGALASICYNIPTPAVDGNVFRIYGRL-------FEIEDDISKG 164
++ LL KG+G +A A+ VD + +L E++ KG
Sbjct: 118 VTREWLLDQKGIGKESADAILCYACAKEVMVVDKYSYLFLKKLGIEIEDYDELQHFFEKG 177
Query: 165 KTKVVYETLVSKTMSQTNAR---EFNQALMDLGATVC 198
+ + L + + A+ F+ +++
Sbjct: 178 VQENLNSALALYENTISLAQLYARFHGKIVEFSKQKL 214
>3fhg_A Mjogg, N-glycosylase/DNA lyase, DNA-(apurinic; helix-hairpin-helix,
8-oxoguanine, 8-OXOG, DNA damage, DNA repair,
glycosidase, hydrolase; 1.90A {Sulfolobus solfataricus}
Length = 207
Score = 48.8 bits (116), Expect = 6e-07
Identities = 19/118 (16%), Positives = 43/118 (36%), Gaps = 9/118 (7%)
Query: 85 GLGYY-SRVRNFQAGCRQVIEQFGGEVPRD--------KKQLLSIKGVGDYTAGALASIC 135
+Y + + +V + E+ +++LL+IKG+G A
Sbjct: 78 KYRFYNLKAKYIIMAREKVYGRLKEEIKPLADEDQQLARERLLNIKGIGMQEASHFLRNV 137
Query: 136 YNIPTPAVDGNVFRIYGRLFEIEDDISKGKTKVVYETLVSKTMSQTNAREFNQALMDL 193
+D ++ R+ I + K +K +Y + + S + + ++DL
Sbjct: 138 GYFDLAIIDRHIIDFMRRIGAIGETNVKQLSKSLYISFENILKSIASNLNMSVGILDL 195
>3hhj_A Mutator MUTT protein; niaid, ssgcid, decode, UW, SBRI, infectious
diseases, hydrol structural genomics; 2.10A {Bartonella
henselae}
Length = 158
Score = 43.9 bits (104), Expect = 1e-05
Identities = 29/143 (20%), Positives = 48/143 (33%), Gaps = 12/143 (8%)
Query: 213 FCSAYKNNTIENFPVKLGKTKVKDVFLLTVV--VKTDTNKYLIQKRPTTGLLSNFYMF-- 268
+ T+E G +K L+ V + N+ L+ +RP L+ + F
Sbjct: 3 HHHHHHMGTLEAQTQGPGSMPIKSSLLIVVACALLDQDNRVLLTQRPEGKSLAGLWEFPG 62
Query: 269 --LSFESD-TPYTSQVEFLSENLPFKVNLNE-KCLGNVKHVFSHLKWNMDVYSGTAKEKT 324
+ E TP S + L E L V + L H + M +Y + +
Sbjct: 63 GKV--EQGETPEASLIRELEEELGVHVQADNLFPLTFASHGYETFHLLMPLYFCSHYKGV 120
Query: 325 IPAN--KTYKLITETQMKKYAFP 345
+ K I + KY P
Sbjct: 121 AQGREGQNLKWIFINDLDKYPMP 143
>3ees_A Probable pyrophosphohydrolase; nudix, RNA pyrophosphohydrolase;
1.90A {Bdellovibrio bacteriovorus} PDB: 3eeu_A 3ef5_A*
3ffu_A*
Length = 153
Score = 42.6 bits (101), Expect = 3e-05
Identities = 25/164 (15%), Positives = 53/164 (32%), Gaps = 37/164 (22%)
Query: 219 NNTIENFPVKLGKTKVKDVFLLTVVVKTDTNKYLIQKRPTTGLLSNFYMFLSFESDTPYT 278
++ +E+ K K + ++ ++ D K L+ +RP L+ +
Sbjct: 4 DSAVESKQKKSKIRKGHWIPVVAGFLRKD-GKILVGQRPENNSLAGQW------------ 50
Query: 279 SQVEF------------------LSENLPFKVNLNEKCLGNVKHVFSHLKWNMDVYSGTA 320
EF L+E L + + E H + + + Y
Sbjct: 51 ---EFPGGKIENGETPEEALARELNEELGIEAEVGEL-KLACTHSYGDVGILILFYEILY 106
Query: 321 KEKTIPA--NKTYKLITETQMKKYAFPVPYQKVWKLFTKSKGLK 362
+ A + + I ++K P +K+ K+ GL+
Sbjct: 107 WKGEPRAKHHMMLEWIHPEELKHRNIPEANRKILHKIYKALGLE 150
>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 = 44.5 bits (104), Expect = 5e-05
Identities = 50/373 (13%), Positives = 104/373 (27%), Gaps = 97/373 (26%)
Query: 36 PYYVWISEVM------LQQTQV-------------KTVLPYYEKFIKTYPTIKDFAF--- 73
Y V + L + + KT + +Y F
Sbjct: 128 KYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVA--LDVCLSYKVQCKMDFKIF 185
Query: 74 -------DTEDNVLKMWEGLGYYSRVRNFQAGCRQV--IEQFGGEVPRDKKQLLSIKGVG 124
++ + VL+M + L Y N+ + I+ + + ++LL K
Sbjct: 186 WLNLKNCNSPETVLEMLQKL-LYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSK--- 241
Query: 125 DYTAGALASICYNIPTPAVDGNVF----RIY--GRLFEIEDDISKGKTKVVYETLVSKTM 178
Y L + N+ N F +I R ++ D +S T + S T+
Sbjct: 242 PYENCLL--VLLNVQNAKA-WNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTL 298
Query: 179 SQTNAREF-----NQALMDLGATVCLFKNPK--CKECPL--SRFCSAYKN--NTIENFPV 227
+ + + DL P+ P S + ++ T +N+
Sbjct: 299 TPDEVKSLLLKYLDCRPQDL---------PREVLTTNPRRLSIIAESIRDGLATWDNWK- 348
Query: 228 KLGKTKVKDVFLLTVVVKTDTNKYLIQKRPTTGLLSNFYMFLSFESDTPYTSQV------ 281
+ K+ + ++ +K F F + +
Sbjct: 349 HVNCDKLTTIIESSL---NVLEPAEYRKM--------FDRLSVFPPSAHIPTILLSLIWF 397
Query: 282 EFLSENLPFKVN-LNEKCLGNVKHVFSHLKWNMDVYSGTAKEKTIPANKTY---KLITET 337
+ + ++ VN L++ L K +Y + K N+ ++
Sbjct: 398 DVIKSDVMVVVNKLHKYSLVE-KQPKESTISIPSIYL---ELKVKLENEYALHRSIVD-- 451
Query: 338 QMKKYAFPVPYQK 350
Y P +
Sbjct: 452 ---HYNIPKTFDS 461
>3n0u_A Probable N-glycosylase/DNA lyase; structural genomics, ISFI, DNA
repair, 8-oxoguanine, base EX repair, PSI-2, protein
structure initiative; 1.50A {Thermotoga maritima}
Length = 219
Score = 38.9 bits (90), Expect = 0.001
Identities = 18/104 (17%), Positives = 37/104 (35%), Gaps = 2/104 (1%)
Query: 91 RVRNFQAGCRQVIEQFGGEVPRDKKQLL-SIKGVGDYTAGALASICYNIPTPAVDGNVFR 149
+ + ++ G+ + ++ L+ + KG+G A +D +V R
Sbjct: 105 FIVENRKLLGKLKNLVKGDPFQSREFLVRNAKGIGWKEASHFLRNTGVEDLAILDKHVLR 164
Query: 150 IYGRLFEIEDDISKGKTKVVYETLVSKTMSQTNAREFNQALMDL 193
+ R + +I KG +K Y + A + DL
Sbjct: 165 LMKRHG-LIQEIPKGWSKKRYLYVEEILRKVAEAFGESPGKFDL 207
>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 = 35.9 bits (82), Expect = 0.017
Identities = 29/158 (18%), Positives = 54/158 (34%), Gaps = 29/158 (18%)
Query: 35 NPYYVWISEVMLQQTQVKTVLPYYEKFIKTY---------------PTIKDFAFDTEDNV 79
+P S + + + E+ + + P+++ A +
Sbjct: 151 DPIECLFSFICSSNNNIARITGMVERLCQAFGPRLIQLDDVTYHGFPSLQALAGPEVEAH 210
Query: 80 LKMWEGLGYYSRVRNFQAGCRQVIEQFGGEVPRD----------KKQLLSIKGVGDYTAG 129
L+ GLGY R R A R ++E+ GG K L + GVG A
Sbjct: 211 LRK-LGLGY--RARYVSASARAILEEQGGLAWLQQLRESSYEEAHKALCILPGVGTCVAD 267
Query: 130 ALASICYNIP-TPAVDGNVFRIYGRLFEIEDDISKGKT 166
+ + + P V+ +++ I R + S+ K
Sbjct: 268 KICLMALDKPQAVPVNVHMWHIAQRDYSWHPTTSQAKG 305
>2rrk_A ORF135, CTP pyrophosphohydrolase; NMR {Escherichia coli}
Length = 140
Score = 34.1 bits (79), Expect = 0.019
Identities = 18/138 (13%), Positives = 39/138 (28%), Gaps = 39/138 (28%)
Query: 228 KLGKTKVKDVFLLTVVVKTDTNKYLIQKRPTTGLLSNFYMFLSFESDTPYTSQVEF---- 283
LG K+ +V + K L+ +RP + + EF
Sbjct: 2 PLGSMKMIEV---VAAIIERDGKILLAQRPAQSDQAGLW---------------EFAGGK 43
Query: 284 --------------LSENLPFKVNLNEKCLGNVKHVFSHLKWNMDVYSGTAKEKTIPAN- 328
L E L + + E + + + S ++ + T+ A+
Sbjct: 44 VEPDESQRQALVRELREELGIEATVGEY-VASHQREVSGRIIHLHAWHVPDFHGTLQAHE 102
Query: 329 -KTYKLITETQMKKYAFP 345
+ + + +Y
Sbjct: 103 HQALVWCSPEEALQYPLA 120
>3fhf_A Mjogg, N-glycosylase/DNA lyase, DNA-(apurinic; helix-hairpin-helix,
8-oxoguanine, 8-OXOG, DNA damage, DNA repair,
glycosidase; 2.00A {Methanocaldococcus jannaschii} PDB:
3knt_A*
Length = 214
Score = 32.3 bits (73), Expect = 0.15
Identities = 16/94 (17%), Positives = 33/94 (35%), Gaps = 1/94 (1%)
Query: 100 RQVIEQFGGEVPRDKKQLLSIKGVGDYTAGALASICYNIPTPAVDGNVFRIYGRLFEIED 159
+ ++E F E + + +IKG+G A +D ++ R D
Sbjct: 110 KDIVESFENEKVAREFLVRNIKGIGYKEASHFLRNVGYDDVAIIDRHILRELYENN-YID 168
Query: 160 DISKGKTKVVYETLVSKTMSQTNAREFNQALMDL 193
+I K ++ Y + + + +DL
Sbjct: 169 EIPKTLSRRKYLEIENILRDIGEEVNLKLSELDL 202
>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 = 29.9 bits (66), Expect = 0.66
Identities = 8/28 (28%), Positives = 10/28 (35%), Gaps = 9/28 (32%)
Query: 322 EKTIPANKTYKLITETQMKKYAFP--VP 347
EK KL + +K YA P
Sbjct: 18 EK----QALKKL--QASLKLYA-DDSAP 38
>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 = 29.6 bits (66), Expect = 2.2
Identities = 24/100 (24%), Positives = 36/100 (36%), Gaps = 24/100 (24%)
Query: 261 LLSNFYMFL-----SFESDTPYTSQVEFLSENLPFKVNLNEK--------CLGNVKHVF- 306
L F L F +D T+ E + + L + +L E L F
Sbjct: 33 LQEQFNKILPEPTEGFAADDEPTTPAELVGKFLGYVSSLVEPSKVGQFDQVLNLCLTEFE 92
Query: 307 -SHLKWNMDVYSGTAK---EKTIPANKTYKLITETQMKKY 342
+L+ N D+++ AK E KT +LI K Y
Sbjct: 93 NCYLEGN-DIHALAAKLLQENDTTLVKTKELI-----KNY 126
Score = 29.6 bits (66), Expect = 2.3
Identities = 21/147 (14%), Positives = 34/147 (23%), Gaps = 46/147 (31%)
Query: 51 VKTVLPYYEK----------FIKTYPTIKDFAFDTEDNVLKMWEGLGYY-SRV------- 92
+ L +E D ++K Y +R+
Sbjct: 84 LNLCLTEFENCYLEGNDIHALAAKLLQENDTTLVKTKELIK-----NYITARIMAKRPFD 138
Query: 93 --------RNFQAGCRQVIEQFGGEVPRDKKQLLSIKGVGDYTAGALASICYNIPTPAVD 144
R G Q++ FGG Q G D L + Y V
Sbjct: 139 KKSNSALFRAVGEGNAQLVAIFGG-------Q-----GNTDDYFEELRDL-YQTYHVLVG 185
Query: 145 GNVFRIYGRLFEIEDDISKGKTKVVYE 171
+ L E+ + V+
Sbjct: 186 DLIKFSAETLSELIRTTL--DAEKVFT 210
>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 = 29.1 bits (65), Expect = 2.3
Identities = 20/146 (13%), Positives = 45/146 (30%), Gaps = 24/146 (16%)
Query: 35 NPYYVWISEVMLQQTQVKTVLPYYEKFIKTY------PTIKDFAFDTEDNVLKM----WE 84
+P+ + +S ++ ++ + + +AF T D + + +E
Sbjct: 114 DPFEILLSFIISANNRIPMIKKCINNISEKAGKKLEYKGKIYYAFPTVDKLHEFTEKDFE 173
Query: 85 GLGYYSRVRNFQAGCRQVIEQFGGEVPRD----------KKQLLSIKGVGDYTAGALASI 134
R + + ++ GE+ + ++L GVG A +
Sbjct: 174 ECTAGFRAKYLKDTVDRIYN---GELNLEYIKSLNDNECHEELKKFMGVGPQVADCIMLF 230
Query: 135 CYNIP-TPAVDGNVFRIYGRLFEIED 159
VD V + L+ D
Sbjct: 231 SMQKYSAFPVDTWVKKAMMSLYVAPD 256
>2z3g_A Blasticidin-S deaminase; hydrolase, cytidine deaminase family,
zinc, tetramer; HET: TRE; 1.50A {Aspergillus terreus}
SCOP: c.97.1.1 PDB: 1wn6_A* 1wn5_A* 2z3h_A* 2z3j_A
2z3i_A*
Length = 130
Score = 27.5 bits (61), Expect = 3.8
Identities = 4/14 (28%), Positives = 6/14 (42%)
Query: 98 GCRQVIEQFGGEVP 111
CRQV+ +
Sbjct: 90 RCRQVLLDLHPGIK 103
>2fr5_A Cytidine deaminase; tetrahydrouridine, protein-inhibitor COM
alternate conformation of Arg68, hydrolase; HET: TYU;
1.48A {Mus musculus} SCOP: c.97.1.1 PDB: 1zab_A* 2fr6_A*
1mq0_A*
Length = 146
Score = 27.5 bits (61), Expect = 4.4
Identities = 6/14 (42%), Positives = 9/14 (64%)
Query: 98 GCRQVIEQFGGEVP 111
CRQV+ +FG +
Sbjct: 101 ACRQVMREFGTDWA 114
>2z0b_A GDE5, KIAA1434, putative glycerophosphodiester phosphodiesterase;
CBM20 domain, starch-binding, hydrolase, STR genomics,
NPPSFA; 2.00A {Homo sapiens}
Length = 131
Score = 27.2 bits (60), Expect = 4.5
Identities = 15/88 (17%), Positives = 28/88 (31%), Gaps = 5/88 (5%)
Query: 20 WYKQNARQLPWRESNNPYYVWISEVMLQQTQVKTVLPYYEKFIKTYPTIKDFAFDTEDNV 79
W QNA L +W + ++L + + Y ++ K Y +
Sbjct: 37 WNPQNAVALLPENDTGESMLWKATIVLSR---GVSVQY--RYFKGYFLEPKTIGGPCQVI 91
Query: 80 LKMWEGLGYYSRVRNFQAGCRQVIEQFG 107
+ WE + ++ QFG
Sbjct: 92 VHKWETHLQPRSITPLESEIIIDDGQFG 119
>2aee_A OPRT, oprtase, orotate phosphoribosyltransferase; structural
genomics, PSI, structure initiative; 1.95A
{Streptococcus pyogenes} SCOP: c.61.1.1
Length = 211
Score = 27.7 bits (62), Expect = 5.3
Identities = 20/103 (19%), Positives = 33/103 (32%), Gaps = 12/103 (11%)
Query: 100 RQVIEQFGGEVPRDKKQLLSIKGVGDYTAGALAS-ICYNIPTPAVDGNVFRI----YGRL 154
+ F + ++ I G + I + P R +G
Sbjct: 52 DLIENGFVETIKAHFPEVEVIAGTA-TAGIPHGAIIADKMTLPFA---YIRSKPKDHGAG 107
Query: 155 FEIEDDISKGKTKVVYETLVSKTMSQTNAREFNQALMDLGATV 197
+IE + KG+ V+ E L+S S + A GA V
Sbjct: 108 NQIEGRVLKGQKMVIIEDLISTGGS---VLDAAAAASREGADV 147
>3oj6_A Blasticidin-S deaminase; ssgcid, seattle structural genomics for
infectious disease, hydrolase; 1.70A {Coccidioides
immitis}
Length = 158
Score = 27.2 bits (60), Expect = 5.6
Identities = 4/14 (28%), Positives = 6/14 (42%)
Query: 98 GCRQVIEQFGGEVP 111
CRQV+ +
Sbjct: 114 RCRQVLADLHPGIK 127
>3m3h_A OPRT, oprtase, orotate phosphoribosyltransferase; pyrimidine
ribonucleotide biosynthesis, structural genomics,
infectious diseases; 1.75A {Bacillus anthracis} PDB:
3osc_A*
Length = 234
Score = 27.4 bits (61), Expect = 6.4
Identities = 22/103 (21%), Positives = 36/103 (34%), Gaps = 12/103 (11%)
Query: 100 RQVIEQFGGEVPRDKKQLLSIKGVGDYTAGALAS-ICYNIPTPAVDGNVFRI----YGRL 154
+ + + + I G A A+ + + P R +G+
Sbjct: 72 QTIAAGLEELIKEHFPTVEVIAGTA-TAGIAHAAWVSDRMDLPMC---YVRSKAKGHGKG 127
Query: 155 FEIEDDISKGKTKVVYETLVSKTMSQTNAREFNQALMDLGATV 197
+IE KG+ VV E L+S S A +AL + G V
Sbjct: 128 NQIEGKAEKGQKVVVVEDLISTGGS---AITCVEALREAGCEV 167
>2gk6_A Regulator of nonsense transcripts 1; UPF1, helicase, NMD,
hydrolase; HET: ADP; 2.40A {Homo sapiens} PDB: 2gjk_A*
2gk7_A 2xzo_A* 2xzp_A
Length = 624
Score = 27.9 bits (62), Expect = 6.6
Identities = 9/29 (31%), Positives = 15/29 (51%)
Query: 275 TPYTSQVEFLSENLPFKVNLNEKCLGNVK 303
TPY Q +L + + F +L+ K V+
Sbjct: 504 TPYEGQRSYLVQYMQFSGSLHTKLYQEVE 532
>2wjy_A Regulator of nonsense transcripts 1; nonsense mediated decay,
zinc-finger, ATP-binding, metal-BIN UPF2, UPF1,
helicase, hydrolase; 2.50A {Homo sapiens} PDB: 2wjv_A
2iyk_A
Length = 800
Score = 28.0 bits (62), Expect = 6.8
Identities = 9/29 (31%), Positives = 15/29 (51%)
Query: 275 TPYTSQVEFLSENLPFKVNLNEKCLGNVK 303
TPY Q +L + + F +L+ K V+
Sbjct: 680 TPYEGQRSYLVQYMQFSGSLHTKLYQEVE 708
>2kv2_A Bloom syndrome protein; HRDC domain, disease mutation, DNA
replicati binding, nucleotide-binding, nucleus, gene
regulation; NMR {Homo sapiens}
Length = 85
Score = 25.6 bits (57), Expect = 8.6
Identities = 6/16 (37%), Positives = 8/16 (50%)
Query: 111 PRDKKQLLSIKGVGDY 126
D + LL I GV +
Sbjct: 45 SSDPEVLLQIDGVTED 60
>2xzl_A ATP-dependent helicase NAM7; hydrolase-RNA complex, NMD, RNA
degradation, allosteric REGU; HET: ADP 1PE; 2.40A
{Saccharomyces cerevisiae}
Length = 802
Score = 27.2 bits (60), Expect = 9.4
Identities = 6/29 (20%), Positives = 14/29 (48%)
Query: 275 TPYTSQVEFLSENLPFKVNLNEKCLGNVK 303
TPY Q ++ + + +L++ V+
Sbjct: 682 TPYEGQRAYILQYMQMNGSLDKDLYIKVE 710
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
0.319 0.134 0.401
Gapped
Lambda K H
0.267 0.0649 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 5,298,656
Number of extensions: 301496
Number of successful extensions: 683
Number of sequences better than 10.0: 1
Number of HSP's gapped: 666
Number of HSP's successfully gapped: 38
Length of query: 363
Length of database: 6,701,793
Length adjustment: 95
Effective length of query: 268
Effective length of database: 4,049,298
Effective search space: 1085211864
Effective search space used: 1085211864
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 58 (26.3 bits)