RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 026681
(235 letters)
>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 = 151 bits (383), Expect = 6e-46
Identities = 33/220 (15%), Positives = 80/220 (36%), Gaps = 36/220 (16%)
Query: 2 KTLEPVYSLGVDETDSSLP-PKERRFAVLLSALLSSLTKDKVADGALQRL------LQNG 54
+ L+ + SL + + + P +F LL A+L+ TK + +L+ L +
Sbjct: 6 EILKALKSLDLLKNAPAWWWPNALKFEALLGAVLTQNTKFEAVLKSLENLKNAFILENDD 65
Query: 55 LHTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKICLTKYDG----DIPSSLDELLA 110
+ I + + + + + P FY +KA + ++ L + + + LL
Sbjct: 66 EINLKKIAYIEFSKLAECVRPSGFYNQKAKRLIDLSGNILKDFQSFENFKQEVTREWLLD 125
Query: 111 LPGIGPKMANMVMTLGWFNVQGICVDTHVHRICNRLGWVTQPGTKQKTSSPEQTREALQR 170
GIG + A+ ++ + + VD + + +LG + ++ + ++
Sbjct: 126 QKGIGKESADAILCYA-CAKEVMVVDKYSYLFLKKLGIEIE--------DYDELQHFFEK 176
Query: 171 WLPKEE----------------WVRINPLLVGFGQTICTP 194
+ + + R + +V F +
Sbjct: 177 GVQENLNSALALYENTISLAQLYARFHGKIVEFSKQKLEL 216
>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 = 149 bits (378), Expect = 4e-45
Identities = 50/170 (29%), Positives = 80/170 (47%), Gaps = 7/170 (4%)
Query: 57 TAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKICLTKYDGDIPSSLDELLALPGIGP 116
T ++ I + Y KA N++K+ + + KY+G++P DEL+ LPG+G
Sbjct: 64 TPHDYIAVPLEELEQDIRSIGLYRNKARNIQKLCAMLIDKYNGEVPRDRDELMKLPGVGR 123
Query: 117 KMANMVMTLGWFNVQGICVDTHVHRICNRLGWVTQPGTKQKTSSPEQTREALQRWLPKEE 176
K AN+V++ F V I VDTHV R+ RLG+ S + + L + +PKEE
Sbjct: 124 KTANVVVS-VAFGVPAIAVDTHVERVSKRLGFCRW------DDSVLEVEKTLMKIIPKEE 176
Query: 177 WVRINPLLVGFGQTICTPLRPRCGMCTVSEYCPSAFKESSTSSSKSKKSE 226
W + ++ FG+ C P+C C + C K K+ +
Sbjct: 177 WSITHHRMIFFGRYHCKAQSPQCPSCPLLHLCREGKKRMRKREEKAANQK 226
>2abk_A Endonuclease III; DNA-repair, DNA glycosylase; 1.85A {Escherichia
coli} SCOP: a.96.1.1
Length = 211
Score = 146 bits (371), Expect = 3e-44
Identities = 51/157 (32%), Positives = 76/157 (48%), Gaps = 8/157 (5%)
Query: 57 TAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKICLTKYDGDIPSSLDELLALPGIGP 116
T A+ + +K I + Y KA N+ K +I L +++G++P L ALPG+G
Sbjct: 60 TPAAMLELGVEGVKTYIKTIGLYNSKAENIIKTCRILLEQHNGEVPEDRAALEALPGVGR 119
Query: 117 KMANMVMTLGWFNVQGICVDTHVHRICNRLGWVTQPGTKQKTSSPEQTREALQRWLPKEE 176
K AN+V+ F I VDTH+ R+CNR + K EQ E L + +P E
Sbjct: 120 KTANVVLNT-AFGWPTIAVDTHIFRVCNRTQF-----APGKN--VEQVEEKLLKVVPAEF 171
Query: 177 WVRINPLLVGFGQTICTPLRPRCGMCTVSEYCPSAFK 213
V + L+ G+ C +PRCG C + + C K
Sbjct: 172 KVDCHHWLILHGRYTCIARKPRCGSCIIEDLCEYKEK 208
>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 = 104 bits (260), Expect = 7e-28
Identities = 34/185 (18%), Positives = 62/185 (33%), Gaps = 33/185 (17%)
Query: 21 PKERRFAVLLSALLSSLTKDKVADGALQRLLQNGLHTAEAIDKADEATIKDLIYPV--AF 78
+E F L LL++ + A AL L Q A+E I++++ F
Sbjct: 29 NEEVWFRELTLCLLTANSSFISAYQALNCLGQKIY-------YANEEEIRNILKSCKYRF 81
Query: 79 YTRKACNMKKIAKICLTKYDGDIPSSLDE--------LLALPGIGPKMANMVMTLGWFNV 130
Y KA + + + +I DE LL + GIG + A+ +
Sbjct: 82 YNLKAKYIIMAREKVYGRLKEEIKPLADEDQQLARERLLNIKGIGMQEASHFL-RNVGYF 140
Query: 131 QGICVDTHVHRICNRLGWVTQPGTKQKTSSPEQTREALQRWLPKEEWVRINPLLVGFGQT 190
+D H+ R+G + + KQ + K ++ +L
Sbjct: 141 DLAIIDRHIIDFMRRIGAIGETNVKQLS---------------KSLYISFENILKSIASN 185
Query: 191 ICTPL 195
+ +
Sbjct: 186 LNMSV 190
>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 = 90.7 bits (226), Expect = 2e-22
Identities = 36/139 (25%), Positives = 64/139 (46%), Gaps = 5/139 (3%)
Query: 79 YTRKACNMKKIAKICLTKYDGDIPSSLDELLALPGIGPKMANMVMTLGWFNVQGICVDTH 138
++A +K++A++ + Y G +P + +L LPG+G VM L F + VD +
Sbjct: 88 SNQRAEQLKELARVVINDYGGRVPRNRKAILDLPGVGKYTCAAVMCLA-FGKKAAMVDAN 146
Query: 139 VHRICNRLGWVTQPGTKQKTSSPEQTREALQRWLPKEEWVRINPLLVGFGQTICTPLRPR 198
R+ NR + + E + +P + N L+ F IC P +P+
Sbjct: 147 FVRVINRYFGGSYENLNYNH---KALWELAETLVPGGKCRDFNLGLMDFSAIICAPRKPK 203
Query: 199 CGMCTVSEYCPSAFKESST 217
C C +S+ C S +++ ST
Sbjct: 204 CEKCGMSKLC-SYYEKCST 221
>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 = 85.9 bits (212), Expect = 9e-21
Identities = 25/181 (13%), Positives = 58/181 (32%), Gaps = 30/181 (16%)
Query: 21 PKERRFAVLLSALLSSLTKDKVADGALQRLLQNGLHTAEAIDKADEATIKDLIYPV--AF 78
+E F L +L++ + A + + + + + + V +
Sbjct: 46 TEEDLFCELSFCVLTANWSAEGGIRAQKEIGKG-------FVHLPLEELAEKLREVGHRY 98
Query: 79 YTRKACNMKKIAKIC---LTKYDGDIPSSLDELLA-LPGIGPKMANMVMTLGWFNVQGIC 134
++A + + K+ GD S + L+ GIG K A+ +
Sbjct: 99 PQKRAEFIVENRKLLGKLKNLVKGDPFQSREFLVRNAKGIGWKEASHFL-RNTGVEDLAI 157
Query: 135 VDTHVHRICNRLGWVTQPGTKQKTSSPEQTREALQRWLPKEEWVRINPLLVGFGQTICTP 194
+D HV R+ R G + + + + K+ ++ + +L +
Sbjct: 158 LDKHVLRLMKRHGLIQE----------------IPKGWSKKRYLYVEEILRKVAEAFGES 201
Query: 195 L 195
Sbjct: 202 P 202
>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 = 82.2 bits (204), Expect = 2e-19
Identities = 38/153 (24%), Positives = 65/153 (42%), Gaps = 15/153 (9%)
Query: 78 FYTRKACNMKKIAKICLTKYDGDIPSSLDELLALPGIGPKMANMVMTLGWFNVQGICVDT 137
+Y R A N+ K A+ T + G P + +E+ ALPG+G A +++L +D
Sbjct: 82 YYAR-ARNLHKAAQQVATLHGGKFPETFEEVAALPGVGRSTAGAILSLS-LGKHFPILDG 139
Query: 138 HVHRICNRL----GWVTQPGTKQKTSSPEQTREALQRWLPKEEWVRINPLLVGFGQTICT 193
+V R+ R GW + + + ++ P R N ++ G ICT
Sbjct: 140 NVKRVLARCYAVSGWPGKKEVEN------KLWSLSEQVTPAVGVERFNQAMMDLGAMICT 193
Query: 194 PLRPRCGMCTVSEYCPSAFKESSTSS--SKSKK 224
+P+C +C + C A +S + K K
Sbjct: 194 RSKPKCSLCPLQNGC-IAAANNSWALYPGKKPK 225
>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 = 82.8 bits (205), Expect = 8e-19
Identities = 45/152 (29%), Positives = 68/152 (44%), Gaps = 15/152 (9%)
Query: 79 YTRKACNMKKIAKICLTKYDGDIPSSLDELLALPGIGPKMANMVMTLGWFNVQGICVDTH 138
Y+R N+ K T+Y G +P DE L G+GP V++L + V VD +
Sbjct: 92 YSR-VRNLHAAVKEVKTRYGGKVPDDPDEFSRLKGVGPYTVGAVLSLA-YGVPEPAVDGN 149
Query: 139 VHRICNRL----GWVTQPGTKQKTSSPEQTREALQRWLPKEEWVRINPLLVGFGQTICTP 194
V R+ +RL + +P T++ + + ++ + E N L+ G +CTP
Sbjct: 150 VMRVLSRLFLVTDDIAKPSTRK------RFEQIVREIMAYENPGAFNEALIELGALVCTP 203
Query: 195 LRPRCGMCTVSEYCPSAFKESSTSS--SKSKK 224
RP C +C V YC AF E K KK
Sbjct: 204 RRPSCLLCPVQAYC-QAFAEGVAEELPVKMKK 234
>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 = 76.9 bits (190), Expect = 5e-17
Identities = 34/155 (21%), Positives = 58/155 (37%), Gaps = 16/155 (10%)
Query: 79 YTRKACNMKKIAKICLTKYDGDIPSSLDELLA-LPGIGPKMANMVMTLGWFNVQGICVDT 137
Y+R +++ A+ + + G +P + + L LPG+G A + ++ F VD
Sbjct: 102 YSR-GRRLQEGARKVVEELGGHMPRTAETLQQLLPGVGRYTAGAIASIA-FGQATGVVDG 159
Query: 138 HVHRICNRL----GWVTQPGTKQKTSSPEQTREALQRWLPKEEWVRINPLLVGFGQTICT 193
+V R+ R+ + Q Q Q+ + N + G T+CT
Sbjct: 160 NVARVLCRVRAIGADPSSTLVSQ------QLWGLAQQLVDPARPGDFNQAAMELGATVCT 213
Query: 194 PLRPRCGMCTVSEYCPSAFKESSTSS--SKSKKSE 226
P RP C C V C A + + S
Sbjct: 214 PQRPLCSQCPVESLC-RARQRVEQEQLLASGSLSG 247
>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 = 64.3 bits (156), Expect = 9e-13
Identities = 22/154 (14%), Positives = 51/154 (33%), Gaps = 18/154 (11%)
Query: 21 PKERRFAVLLSALLSSLTKDKVADGALQRLLQNGLHTAEAIDKADEATIKDLIYPVA--F 78
E F L +L++ + + + L +++ + + F
Sbjct: 40 SNEEWFKELCFCILTANFTAEGGIRIQKEIGDGFL-------TLPREELEEKLKNLGHRF 92
Query: 79 YTRKACNMKKIAKICLTKYDGDIPSSLDE-----LLALPGIGPKMANMVMTLGWFNVQGI 133
Y ++A + + K + + + + GIG K A+ + ++ I
Sbjct: 93 YRKRAEYIVLARRFKNIKDIVESFENEKVAREFLVRNIKGIGYKEASHFLRNVGYDDVAI 152
Query: 134 CVDTHVHRICNRLGWVTQPGTKQKTSSPEQTREA 167
+D H+ R ++ + KT S + E
Sbjct: 153 -IDRHILRELYENNYIDE---IPKTLSRRKYLEI 182
>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 = 57.9 bits (140), Expect = 8e-11
Identities = 19/91 (20%), Positives = 38/91 (41%), Gaps = 8/91 (8%)
Query: 26 FAVLLSALLSSLTKDKVADGALQRLLQNGLHTAEAIDKADEATIKDLIYPVAFYTRKACN 85
+ +L++ + + T K+A L + L+ +AE AD + +L+ P+ Y +A
Sbjct: 32 WKLLIATIFLNRTSGKMAIPVLWKFLEK-YPSAEVARTADWRDVSELLKPLGLYDLRAKT 90
Query: 86 MKKIAKICLTKYDGDIPSSLDELLALPGIGP 116
+ K + + + L GIG
Sbjct: 91 IVKFSD-------EYLTKQWKYPIELHGIGK 114
>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 = 54.2 bits (130), Expect = 6e-09
Identities = 22/176 (12%), Positives = 56/176 (31%), Gaps = 35/176 (19%)
Query: 20 PPKERRFAVLLSALLSSLTKDKVADGALQRLLQN-------------GLHTAEAIDKADE 66
++ F +LLS ++S+ + + + + + T + + + E
Sbjct: 110 ILRQDPFEILLSFIISANNRIPMIKKCINNISEKAGKKLEYKGKIYYAFPTVDKLHEFTE 169
Query: 67 ATIKDLIYPVAFYTRKACNMKKIAKICLTK-------YDGDIPSSLDELLALPGIGPKMA 119
++ +A +K + +EL G+GP++A
Sbjct: 170 KDFEECTAG-----FRAKYLKDTVDRIYNGELNLEYIKSLNDNECHEELKKFMGVGPQVA 224
Query: 120 NMVM--TLGWFNVQGICVDTHVHRICNRLGWVTQPGTKQKTSSPEQTREALQRWLP 173
+ +M ++ ++ VDT V + L S + +++
Sbjct: 225 DCIMLFSMQKYSA--FPVDTWVKKAMMSLYVAP------DVSLKKIRDFGREKFGS 272
>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 = 54.4 bits (130), Expect = 7e-09
Identities = 31/174 (17%), Positives = 57/174 (32%), Gaps = 26/174 (14%)
Query: 26 FAVLLSALLSSLTKDKVADGALQRLLQ---NGLHTAEAIDKADEATIKDL-------IYP 75
L S + SS G ++RL Q L + + +++ L
Sbjct: 153 IECLFSFICSSNNNIARITGMVERLCQAFGPRLIQLDDVTYHGFPSLQALAGPEVEAHLR 212
Query: 76 VAFYTRKACNMKKIAKICLTKYDG----------DIPSSLDELLALPGIGPKMANMV--M 123
+A + A+ L + G + L LPG+G +A+ + M
Sbjct: 213 KLGLGYRARYVSASARAILEEQGGLAWLQQLRESSYEEAHKALCILPGVGTCVADKICLM 272
Query: 124 TLGWFNVQGICVDTHVHRICNRLGWVTQPGTKQKTSSPEQTREALQRWLPKEEW 177
L + V+ H+ I R ++ K SP+ +E + + W
Sbjct: 273 ALDKPQA--VPVNVHMWHIAQRDYSWHPTTSQAKGPSPQTNKELGNFF--RSLW 322
>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 = 53.1 bits (127), Expect = 2e-08
Identities = 40/263 (15%), Positives = 80/263 (30%), Gaps = 74/263 (28%)
Query: 2 KTL-EPVYSLGVDETDSSLPPKE--RRFAVLLSALLSSLTK---DKVADGALQR-----L 50
K L EP D+ ++ P E +F +S+L+ D+V + L L
Sbjct: 39 KILPEPTEGFAADDEPTT--PAELVGKFLGYVSSLVEPSKVGQFDQVLNLCLTEFENCYL 96
Query: 51 LQNGLHT-AEAIDKADEATI---KDLIYPVAFYTRKACNMKKI----------------A 90
N +H A + + ++ T+ K+LI + T + + A
Sbjct: 97 EGNDIHALAAKLLQENDTTLVKTKELI--KNYITARIMAKRPFDKKSNSALFRAVGEGNA 154
Query: 91 KICLTKYD-----GDIPSSLDELLAL-----PGIGPKMANMVMTLGWFNVQGICVDTHVH 140
++ G+ +EL L +G + TL + +
Sbjct: 155 QL----VAIFGGQGNTDDYFEELRDLYQTYHVLVGDLIKFSAETLSELIRTTLDAEKVFT 210
Query: 141 RICNRLGWVTQPGTKQKTSSPEQTREALQRWLPKEEWVRINPL---LVGFGQTICTPLRP 197
+ N L W+ P P ++++ P+ L+G Q
Sbjct: 211 QGLNILEWLENPSNT-----------------PDKDYLLSIPISCPLIGVIQLAHY---- 249
Query: 198 RCGMCTVSEYCPSAFKESSTSSS 220
+ + P + ++
Sbjct: 250 -VVTAKLLGFTPGELRSYLKGAT 271
Score = 47.4 bits (112), Expect = 2e-06
Identities = 42/209 (20%), Positives = 67/209 (32%), Gaps = 62/209 (29%)
Query: 3 TLEPVYSLGVDETDSSLPPKE----------RRFAVL------LSALLSSLTKDKVADGA 46
T E V V++T+S LP + + V+ L L +L K K G
Sbjct: 345 TQEQVQDY-VNKTNSHLPAGKQVEISLVNGAKNL-VVSGPPQSLYGLNLTLRKAKAPSGL 402
Query: 47 LQ-------RLLQNGL---------HT---AEAIDKADEATI--------KDLIYPVAFY 79
Q R L+ H+ A D ++ + KD+ PV +
Sbjct: 403 DQSRIPFSERKLKFSNRFLPVASPFHSHLLVPASDLINKDLVKNNVSFNAKDIQIPV-YD 461
Query: 80 TRKACNMKKIAKICLTKYDGDIPSSL-DELLALP----GIGPKMANMVMTLGWFNVQGIC 134
T +++ G I + D ++ LP A ++ G G+
Sbjct: 462 TFDGSDLR--------VLSGSISERIVDCIIRLPVKWETTTQFKATHILDFGPGGASGLG 513
Query: 135 VDTHVHRICNRLGW-VTQPGTKQKTSSPE 162
V T HR + G V GT +
Sbjct: 514 VLT--HRNKDGTGVRVIVAGTLDINPDDD 540
>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 = 43.3 bits (101), Expect = 4e-05
Identities = 34/234 (14%), Positives = 73/234 (31%), Gaps = 64/234 (27%)
Query: 35 SSLTKDKVADGALQRLLQNGLHTAEAIDKADEATIKDLIYPV-AFYTRKACNMKKIAKIC 93
+ + D +Q + + ++ + + + ++ + + N
Sbjct: 164 TWVALDVCLSYKVQCKMDFKIFW---LNLKNCNSPETVLEMLQKLLYQIDPNWTS----- 215
Query: 94 LTKYDGDIPSSLDE-----------------LLALPGI-GPKMANMVMTLGWFNVQGIC- 134
+ + +I + LL L + K N FN+ C
Sbjct: 216 RSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNA------FNLS--CK 267
Query: 135 --VDTHVHRICNRLGWVTQP----GTKQKTSSPEQTREALQRW-------LPKEEWVRIN 181
+ T ++ + L T T +P++ + L ++ LP+E + N
Sbjct: 268 ILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREV-LTTN 326
Query: 182 PLLVG-FGQTICTPLRPRCGMCTVSEYCPSAFKESSTSSSKSKKSESSSLRKLE 234
P + ++I R G+ T + +K + K SSL LE
Sbjct: 327 PRRLSIIAESI------RDGLAT-WDN----WKHVNC--DKLTTIIESSLNVLE 367
Score = 36.4 bits (83), Expect = 0.008
Identities = 26/192 (13%), Positives = 59/192 (30%), Gaps = 64/192 (33%)
Query: 2 KTLEPVYSLG-----VDETDSSLPPKERRFAVLLSALLSSLTKDKVADGALQRLLQNGLH 56
TL P +D LP + + + S+ + +++GL
Sbjct: 296 MTLTPDEVKSLLLKYLDCRPQDLPRE----VLTTNPRRLSI---------IAESIRDGLA 342
Query: 57 TAEAIDKADEATIKDLIYPVAFYTRKACN-MKKIAKICLTKYDGDIPSSLDELLALPGIG 115
T + + C+ + I + L + P+ ++ +
Sbjct: 343 TWD------------------NWKHVNCDKLTTIIESSLNVLE---PAEYRKMFDRLSVF 381
Query: 116 PKMAN---MVMTLGWFNVQGICVDTHVHRICNRLGWVTQPGTKQKTSSPEQTREALQRWL 172
P A+ ++++L WF+V V V+++ +++
Sbjct: 382 PPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYS--------------------LVEKQ- 420
Query: 173 PKEEWVRINPLL 184
PKE + I +
Sbjct: 421 PKESTISIPSIY 432
>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 = 39.8 bits (93), Expect = 3e-04
Identities = 27/123 (21%), Positives = 47/123 (38%), Gaps = 19/123 (15%)
Query: 57 TAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKICLTKY--DGDIPSSLDELLALPGI 114
T EAI KA +++ RKA + +IAK + + + + L + GI
Sbjct: 163 TQEAILKAGVEGLRECGLS----RRKAELIVEIAKEENLEELKEWGEEEAYEYLTSFKGI 218
Query: 115 GPKMANMVMTLGW----FNVQGICVDTHVHRICNRLGWVTQPGTKQKTSSPEQTREALQR 170
G A +V+++ F D V R +RL + S+ + A +R
Sbjct: 219 GRWTAELVLSIALGKNVFPAD----DLGVRRAVSRLY-----FNGEIQSAEKVREIARER 269
Query: 171 WLP 173
+
Sbjct: 270 FGR 272
>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 = 34.0 bits (78), Expect = 0.031
Identities = 19/81 (23%), Positives = 30/81 (37%), Gaps = 11/81 (13%)
Query: 57 TAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKICLTK-----YDGDIPSSLDELLAL 111
T + + AD +K L P ++A + +A L GD+ ++ L
Sbjct: 157 TPQRLAAADPQALKALGMP----LKRAEALIHLANAALEGTLPMTIPGDVEQAMKTLQTF 212
Query: 112 PGIGPKMANMVM--TLGWFNV 130
PGIG AN +V
Sbjct: 213 PGIGRWTANYFALRGWQAKDV 233
>1dgs_A DNA ligase; AMP complex, NAD+-dependent; HET: DNA AMP; 2.90A
{Thermus filiformis} SCOP: a.60.2.2 b.40.4.6 d.142.2.2
PDB: 1v9p_A*
Length = 667
Score = 33.2 bits (77), Expect = 0.058
Identities = 15/84 (17%), Positives = 28/84 (33%), Gaps = 25/84 (29%)
Query: 104 SLDELLALPGIGPKMANMVMTLGWFNVQGICVDTHVHRICNRL---GWVTQPGTKQKTSS 160
SL+EL+ + +G A ++ D + RL G +K++ S
Sbjct: 537 SLEELIEVEEVGELTARAILE--TLK------DPAFRDLVRRLKEAG--VSMESKEEVSD 586
Query: 161 P------------EQTREALQRWL 172
+ RE ++ L
Sbjct: 587 LLSGLTFVLTGELSRPREEVKALL 610
>2duy_A Competence protein comea-related protein; helix-hairpin-helix,
structural genomics, NPPSFA; 1.75A {Thermus
thermophilus} SCOP: a.60.2.7
Length = 75
Score = 30.4 bits (69), Expect = 0.081
Identities = 12/16 (75%), Positives = 15/16 (93%)
Query: 104 SLDELLALPGIGPKMA 119
SL+EL+ALPGIGP +A
Sbjct: 25 SLEELMALPGIGPVLA 40
Score = 25.4 bits (56), Expect = 5.4
Identities = 6/16 (37%), Positives = 11/16 (68%)
Query: 103 SSLDELLALPGIGPKM 118
+ +++LL + GIGP
Sbjct: 50 ARVEDLLKVKGIGPAT 65
>2edu_A Kinesin-like protein KIF22; kinesin-like DNA binding domain, helix
turn helix motif, structural genomics, NPPSFA; NMR {Homo
sapiens} SCOP: a.60.2.7
Length = 98
Score = 30.9 bits (70), Expect = 0.10
Identities = 8/16 (50%), Positives = 10/16 (62%)
Query: 104 SLDELLALPGIGPKMA 119
S +L +L IGPK A
Sbjct: 38 SARDLRSLQRIGPKKA 53
>1u5h_A CITE; TIM barrel, structural genomics, PSI, protein structure
initiative, TB structural genomics consortium, TBSGC,
lyase; 1.65A {Mycobacterium tuberculosis} SCOP: c.1.12.5
PDB: 1u5v_A* 1z6k_A
Length = 273
Score = 31.7 bits (73), Expect = 0.17
Identities = 8/24 (33%), Positives = 10/24 (41%), Gaps = 2/24 (8%)
Query: 162 EQTREALQRWL--PKEEWVRINPL 183
R AL+ P+ VRIN
Sbjct: 45 PAARNALRDTPLDPERTVVRINAG 68
>2owo_A DNA ligase; protein-DNA complex, ligase-DNA complex; HET: DNA OMC
AMP; 2.30A {Escherichia coli}
Length = 671
Score = 31.7 bits (73), Expect = 0.21
Identities = 9/43 (20%), Positives = 19/43 (44%), Gaps = 8/43 (18%)
Query: 104 SLDELLALPGIGPKMANMVMTLGWFNVQGICVDTHVHRICNRL 146
S++EL +P +G +A+ V +F + + + L
Sbjct: 542 SIEELQKVPDVGIVVASHVHN--FFA------EESNRNVISEL 576
>2yg9_A DNA-3-methyladenine glycosidase II, putative; hydrolase, DNA
repair; 1.95A {Deinococcus radiodurans} PDB: 2yg8_A
Length = 225
Score = 31.2 bits (71), Expect = 0.21
Identities = 22/100 (22%), Positives = 33/100 (33%), Gaps = 14/100 (14%)
Query: 41 KVADGALQRLLQ-NGLHTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKICLTK-YD 98
K A RL G A+ K ++ + K ++ A ++ D
Sbjct: 77 KAAQAIYGRLEGLPGGVVPAALLKVSGDDLRGV----GLSWAKVRTVQAAAAAAVSGQID 132
Query: 99 GDIPSSLD------ELLALPGIGPKMANMVM--TLGWFNV 130
S EL+ LPGIG A M + L +V
Sbjct: 133 FAHLSGQPDELVIAELVQLPGIGRWTAEMFLLFALARPDV 172
>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 = 30.8 bits (70), Expect = 0.27
Identities = 17/93 (18%), Positives = 36/93 (38%), Gaps = 13/93 (13%)
Query: 47 LQRLLQNGLHTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKICLTK-YDGDIPSSL 105
+++L+ L E + + + ++ RK ++ + + + D
Sbjct: 76 VEQLVGGALEKPEQLYRVSDEALRQA----GVSKRKIEYIRHVCEHVESGRLDFTELEGA 131
Query: 106 D------ELLALPGIGPKMANMVM--TLGWFNV 130
+ +L A+ GIG A M M +LG +V
Sbjct: 132 EATTVIEKLTAIKGIGQWTAEMFMMFSLGRLDV 164
>3arc_U Photosystem II 12 kDa extrinsic protein; PSII, membrane-protein
complex, transmembrane alpha-helix, E transport,
photosynthesis; HET: OEX CLA PHO BCR PL9 SQD LMG UNL LMT
HTG DGD LHG HEM; 1.90A {Thermosynechococcus vulcanus}
PDB: 3bz1_U* 2axt_U* 3bz2_U* 3kzi_U* 3prq_U* 3prr_U*
3a0b_U* 3a0h_U*
Length = 97
Score = 29.5 bits (66), Expect = 0.30
Identities = 5/38 (13%), Positives = 17/38 (44%), Gaps = 7/38 (18%)
Query: 103 SSLDELLALPGIGPKMANMVMTLGWF-------NVQGI 133
+++ + G+ P +A +++ + N+ G+
Sbjct: 23 TNIAAFIQYRGLYPTLAKLIVKNAPYESVEDVLNIPGL 60
>1s5l_U Photosystem II 12 kDa extrinsic protein; photosynthesis,
oxygen-evolving, tetra- manganese, membrane; HET: CL1
PHO HEM PL9 LMT BCR; 3.50A {Thermosynechococcus
elongatus}
Length = 134
Score = 30.1 bits (67), Expect = 0.33
Identities = 5/38 (13%), Positives = 17/38 (44%), Gaps = 7/38 (18%)
Query: 103 SSLDELLALPGIGPKMANMVMTLGWF-------NVQGI 133
+++ + G+ P +A +++ + N+ G+
Sbjct: 60 TNIAAFIQYRGLYPTLAKLIVKNAPYESVEDVLNIPGL 97
>1kft_A UVRC, excinuclease ABC subunit C; helix-hairpin-helix, HHH domain,
DNA-binding domain, DNA binding protein; NMR
{Escherichia coli} SCOP: a.60.2.3
Length = 78
Score = 28.3 bits (64), Expect = 0.47
Identities = 6/19 (31%), Positives = 12/19 (63%)
Query: 104 SLDELLALPGIGPKMANMV 122
S++E+ +PGI +A +
Sbjct: 54 SVEEIAKVPGISQGLAEKI 72
>1x2i_A HEF helicase/nuclease; alpha helix, helix-hairpin-helix DNA binding
domain, homodimer, hydrolase; 1.45A {Pyrococcus
furiosus} SCOP: a.60.2.5
Length = 75
Score = 28.0 bits (63), Expect = 0.64
Identities = 8/16 (50%), Positives = 12/16 (75%)
Query: 104 SLDELLALPGIGPKMA 119
S+ EL+ + GIG K+A
Sbjct: 44 SVAELMKVEGIGEKIA 59
>3sgi_A DNA ligase; HET: DNA AMP; 3.50A {Mycobacterium tuberculosis}
Length = 615
Score = 30.2 bits (69), Expect = 0.65
Identities = 12/43 (27%), Positives = 18/43 (41%), Gaps = 8/43 (18%)
Query: 104 SLDELLALPGIGPKMANMVMTLGWFNVQGICVDTHVHRICNRL 146
S D+L A+ G+GP +A V WF I ++
Sbjct: 559 STDQLAAVEGVGPTIAAAVTE--WFA------VDWHREIVDKW 593
>2fmp_A DNA polymerase beta; nucleotidyl transferase, transferase/DNA
complex; HET: DNA DOC DCT; 1.65A {Homo sapiens} SCOP:
a.60.6.1 a.60.12.1 d.218.1.2 PDB: 1bpx_A* 1bpz_A*
1mq2_A* 1mq3_A* 1bpy_A* 1tva_A* 1zjm_A* 1zjn_A* 1zqa_A*
1zqb_A* 1zqc_A* 1zqd_A* 1zqe_A* 1zqf_A* 1zqg_A* 1zqh_A*
1zqi_A* 1zqj_A* 1zqk_A* 1zql_A* ...
Length = 335
Score = 29.5 bits (65), Expect = 1.0
Identities = 11/32 (34%), Positives = 15/32 (46%), Gaps = 1/32 (3%)
Query: 94 LTKYDGDIPSSLDELLALPGIGPKMANMVMTL 125
+ KY I S E LPG+G K+A +
Sbjct: 46 IAKYPHKI-KSGAEAKKLPGVGTKIAEKIDEF 76
>1vdd_A Recombination protein RECR; helix-hairpin-helix, zinc finger,
toprim, walker B ATP binding motif; 2.50A {Deinococcus
radiodurans} SCOP: e.49.1.1 PDB: 2v1c_A
Length = 228
Score = 28.7 bits (65), Expect = 1.3
Identities = 13/24 (54%), Positives = 15/24 (62%)
Query: 96 KYDGDIPSSLDELLALPGIGPKMA 119
KY + S + EL LPGIGPK A
Sbjct: 2 KYPPSLVSLIRELSRLPGIGPKSA 25
>2ihm_A POL MU, DNA polymerase MU; helix-turn-helix, transferase/DNA
complex; HET: DNA D3T; 2.40A {Mus musculus}
Length = 360
Score = 29.1 bits (64), Expect = 1.3
Identities = 8/70 (11%), Positives = 20/70 (28%), Gaps = 8/70 (11%)
Query: 87 KKIAKICLTKYDGDI--------PSSLDELLALPGIGPKMANMVMTLGWFNVQGICVDTH 138
+ I ++ ++ ++ + G+G K AN G + +
Sbjct: 75 RVIQELLEHGTCEEVKQVRCSERYQTMKLFTQVFGVGVKTANRWYQEGLRTLDELREQPQ 134
Query: 139 VHRICNRLGW 148
+ G
Sbjct: 135 RLTQQQKAGL 144
>1z00_A DNA excision repair protein ERCC-1; helix-hairpin-helix, hydrolase;
HET: DNA; NMR {Homo sapiens} SCOP: a.60.2.5
Length = 89
Score = 27.5 bits (61), Expect = 1.3
Identities = 7/17 (41%), Positives = 11/17 (64%)
Query: 104 SLDELLALPGIGPKMAN 120
S ++L PG+GP+ A
Sbjct: 49 SREDLALCPGLGPQKAR 65
>1sgj_A Citrate lyase, beta subunit; trimer, TIM barrel, structural
genomics, PSI, protein structure initiative; 1.84A
{Deinococcus radiodurans} SCOP: c.1.12.5
Length = 284
Score = 28.7 bits (65), Expect = 1.5
Identities = 6/36 (16%), Positives = 14/36 (38%), Gaps = 4/36 (11%)
Query: 152 PGTKQKTSSPEQTREALQRWL----PKEEWVRINPL 183
+ K ++ +A + + +VR+N L
Sbjct: 43 GTAEAKAAARPVAHDAARDLIAAAPHLAVFVRVNAL 78
>1gm5_A RECG; helicase, replication restart; HET: DNA ADP; 3.24A
{Thermotoga maritima} SCOP: a.24.21.1 b.40.4.9 c.37.1.19
c.37.1.19
Length = 780
Score = 29.1 bits (66), Expect = 1.5
Identities = 19/102 (18%), Positives = 36/102 (35%), Gaps = 3/102 (2%)
Query: 30 LSALLSSLTKDKVADGALQRLLQNGLHTAEAIDKADEATIKDLIYPVAFYTRKACNMKKI 89
+ LL L + + L+ LQ L + I EA + I K + I
Sbjct: 42 IHQLLKELDDPLLENKDLEEKLQAFLDYVKEIPNLPEARKRYRIQKSLEMIEKLRSWFLI 101
Query: 90 AKICLTKYDGDIPSSLDELLALPGIGPKMANMVMTLGWFNVQ 131
+ + + D+ + + G+GP + LG ++
Sbjct: 102 DYLECSGEEVDLSTDIQYA---KGVGPNRKKKLKKLGIETLR 140
>3pzp_A DNA polymerase kappa; DNA nucleotidyltransferase, DNA binding
nucleotide binding M binding, nucleus; HET: DNA TTD DTP;
3.34A {Homo sapiens}
Length = 517
Score = 28.8 bits (64), Expect = 1.5
Identities = 18/92 (19%), Positives = 29/92 (31%), Gaps = 17/92 (18%)
Query: 55 LHTAEAIDKADEATIKDLIYPVAFYTRKACN--MKKIAKIC--LTKYDG--DIPSSLDEL 108
+ A + E I+ I T A +AK+C K +G I + +
Sbjct: 274 VFGTSAQEVVKE--IRFRIEQKTTLTASAGIAPNTMLAKVCSDKNKPNGQYQILPNRQAV 331
Query: 109 LA---------LPGIGPKMANMVMTLGWFNVQ 131
+ + GIG M+ LG
Sbjct: 332 MDFIKDLPIRKVSGIGKVTEKMLKALGIITCT 363
>2w9m_A Polymerase X; SAXS, DNA repair, DNA polymerase, DNA replication;
2.46A {Deinococcus radiodurans}
Length = 578
Score = 28.9 bits (64), Expect = 1.6
Identities = 11/49 (22%), Positives = 21/49 (42%)
Query: 94 LTKYDGDIPSSLDELLALPGIGPKMANMVMTLGWFNVQGICVDTHVHRI 142
L G +P L +LL + G+GPK + G +++ + +
Sbjct: 85 LEAAAGQLPPGLLDLLGVRGLGPKKIRSLWLAGIDSLERLREAAESGEL 133
Score = 28.1 bits (62), Expect = 3.1
Identities = 6/33 (18%), Positives = 13/33 (39%), Gaps = 1/33 (3%)
Query: 94 LTKYDGDIPS-SLDELLALPGIGPKMANMVMTL 125
L + + + P E +P +G +A +
Sbjct: 44 LEELNEETPELLAREFTGIPKVGKGIAAELSDF 76
>2a1j_B DNA excision repair protein ERCC-1; XPF, xeroderma pigmentosum, DNA
repair, endonuclease, helix-hairpin-helix, DNA binding
protein; HET: DNA; 2.70A {Homo sapiens} SCOP: a.60.2.5
Length = 91
Score = 27.1 bits (60), Expect = 2.1
Identities = 7/17 (41%), Positives = 11/17 (64%)
Query: 104 SLDELLALPGIGPKMAN 120
S ++L PG+GP+ A
Sbjct: 62 SREDLALCPGLGPQKAR 78
>2rhf_A DNA helicase RECQ; HRDC, D. radiodurans, ATP-binding, hydrolase
nucleotide-binding; HET: DNA; 1.10A {Deinococcus
radiodurans}
Length = 77
Score = 26.3 bits (59), Expect = 2.3
Identities = 8/16 (50%), Positives = 11/16 (68%)
Query: 102 PSSLDELLALPGIGPK 117
P +L EL +PG+G K
Sbjct: 43 PRTLAELAEVPGLGEK 58
>3osn_A DNA polymerase IOTA; hoogsteen base PAIR, protein-DNA complex,
Y-family DNA polym translesion synthesis, nucleoside
triphosphate; HET: DNA DOC 6OG TTP; 1.90A {Homo sapiens}
PDB: 2dpj_A* 2fll_A* 2fln_A* 2flp_A* 3epg_A* 3epi_A*
2dpi_A* 3g6v_A* 3g6y_A* 3g6x_A* 3gv7_B* 3gv8_B* 3ngd_A*
3gv5_B* 3q8p_B* 3q8q_B* 3q8r_B* 3q8s_B* 3h4d_A* 3h4b_A*
...
Length = 420
Score = 28.1 bits (63), Expect = 2.4
Identities = 16/56 (28%), Positives = 25/56 (44%), Gaps = 13/56 (23%)
Query: 83 ACNMKKIAKIC--LTKYDG----------DIPSSLDELLALPGIGPKMANMVMTLG 126
A N K +AK+ + K + + SL+ + +PGIG K A + LG
Sbjct: 200 ASN-KLLAKLVSGVFKPNQQTVLLPESCQHLIHSLNHIKEIPGIGYKTAKCLEALG 254
>1t94_A Polymerase (DNA directed) kappa; replication, DNA repair, Y-family
DNA polymerase, translesion DNA synthesis, lesion
bypass; 2.40A {Homo sapiens} SCOP: d.240.1.1 e.8.1.7
PDB: 2oh2_A* 2w7o_A* 2w7p_A* 3hed_A* 3in5_A*
Length = 459
Score = 28.0 bits (62), Expect = 2.8
Identities = 18/91 (19%), Positives = 29/91 (31%), Gaps = 17/91 (18%)
Query: 55 LHTAEAIDKADEATIKDLIYPVAFYTRKAC--NMKKIAKIC--LTKYDG--DIPSSLDEL 108
+ A + E I+ I T A +AK+C K +G I + +
Sbjct: 218 VFGTSAQEVVKE--IRFRIEQKTTLTASAGIAPNTMLAKVCSDKNKPNGQYQILPNRQAV 275
Query: 109 LA---------LPGIGPKMANMVMTLGWFNV 130
+ + GIG M+ LG
Sbjct: 276 MDFIKDLPIRKVSGIGKVTEKMLKALGIITC 306
>3qll_A Citrate lyase; beta barrel; 2.45A {Yersinia pestis}
Length = 316
Score = 28.0 bits (63), Expect = 2.9
Identities = 8/28 (28%), Positives = 11/28 (39%), Gaps = 6/28 (21%)
Query: 162 EQTREALQRWL------PKEEWVRINPL 183
EQ R+ +L +RIN L
Sbjct: 84 EQARQKAISYLSSRPATSLPLALRINGL 111
>3i23_A Oxidoreductase, GFO/IDH/MOCA family; structural genomics, PSI-2,
protein structure initiative, northeast structural
genomics consortium; 2.30A {Enterococcus faecalis} PDB:
3fd8_A* 3hnp_A
Length = 349
Score = 27.6 bits (62), Expect = 3.7
Identities = 7/59 (11%), Positives = 19/59 (32%), Gaps = 9/59 (15%)
Query: 56 HTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKICLTKYDGDIPSSLDELLALPGI 114
+ + + + + ++ + A + + + L+ELL P I
Sbjct: 17 YHLPYVMIRETLEV------KTIFDL---HVNEKAAAPFKEKGVNFTADLNELLTDPEI 66
>2krx_A ASL3597 protein; structural genomics, PSI-2, protein structure
initiative, no structural genomics consortium, NESG,
unknown function; NMR {Nostoc SP}
Length = 94
Score = 26.3 bits (58), Expect = 4.0
Identities = 6/40 (15%), Positives = 14/40 (35%)
Query: 149 VTQPGTKQKTSSPEQTREALQRWLPKEEWVRINPLLVGFG 188
V + ++ + + E L+ L K + + L
Sbjct: 14 VLETNQPEQFLTTIELLEKLKGELEKISFSDLPLELQKLD 53
>2bcq_A DNA polymerase lambda; misalignment, extrahelical, mutagenesis,
mutation, deletion, streisinger, slippage, transferase,
lyase/DNA complex; HET: DNA; 1.65A {Homo sapiens} SCOP:
a.60.6.1 a.60.12.1 d.218.1.2 PDB: 1xsl_A* 2bcr_A*
2bcs_A* 2bcu_A* 2bcv_A* 2gws_A* 3c5g_A* 3c5f_A* 2pfn_A*
1xsp_A* 1xsn_A* 2pfo_A* 2pfp_A* 2pfq_A* 3hw8_A* 3hwt_A*
1rzt_A* 3hx0_A* 3mdc_A* 3mda_A* ...
Length = 335
Score = 27.5 bits (60), Expect = 4.1
Identities = 9/32 (28%), Positives = 18/32 (56%), Gaps = 1/32 (3%)
Query: 94 LTKYDGDIPSSLDELLALPGIGPKMANMVMTL 125
L + + +S E ++PGIG +MA ++ +
Sbjct: 46 LKSFHKPV-TSYQEACSIPGIGKRMAEKIIEI 76
>3e18_A Oxidoreductase; dehydrogenase, NAD-binding, structural genom
protein structure initiative, PSI, NEW YORK structural
GENO research consortium; HET: NAD; 1.95A {Listeria
innocua}
Length = 359
Score = 27.3 bits (61), Expect = 4.9
Identities = 8/57 (14%), Positives = 15/57 (26%), Gaps = 11/57 (19%)
Query: 58 AEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKICLTKYDGDIPSSLDELLALPGI 114
AD + + A + A+ I S + +LA +
Sbjct: 21 VTLASAADNLEV------HGVFDILAEKREAAAQ-----KGLKIYESYEAVLADEKV 66
>2gwn_A Dihydroorotase; zinc-binding prote structural genomics, PSI,
protein structure initiative, MID center for structural
genomics, MCSG; HET: KCX GOL; 1.85A {Porphyromonas
gingivalis}
Length = 452
Score = 27.2 bits (61), Expect = 5.1
Identities = 13/59 (22%), Positives = 17/59 (28%), Gaps = 26/59 (44%)
Query: 88 KIAKICLTKYDGDIPSSLDE------LLALPGIGPKMANMVMTLGWFNVQGICVDTHVH 140
I++I + D S DE L PG C+D VH
Sbjct: 30 FISRIIEGELPADDNLSADEVIECSGLRLFPG--------------------CIDDQVH 68
>1pzn_A RAD51, DNA repair and recombination protein RAD51, RADA; heptameric
ring, heptamer, ring, oligomer, RAD51 polymerizat motif;
HET: DNA; 2.85A {Pyrococcus furiosus} SCOP: a.60.4.1
c.37.1.11
Length = 349
Score = 26.9 bits (59), Expect = 5.7
Identities = 10/41 (24%), Positives = 17/41 (41%)
Query: 95 TKYDGDIPSSLDELLALPGIGPKMANMVMTLGWFNVQGICV 135
T + + LPG+GP A + G+ ++ I V
Sbjct: 24 TPKKKKKEKIIRSIEDLPGVGPATAEKLREAGYDTLEAIAV 64
>2kp7_A Crossover junction endonuclease MUS81; helix-hairpin-helix, tumour
suppressor, DNA damage, DNA recombination, DNA repair,
hydrolase, magnesium; NMR {Mus musculus}
Length = 87
Score = 25.7 bits (56), Expect = 5.9
Identities = 9/42 (21%), Positives = 16/42 (38%), Gaps = 1/42 (2%)
Query: 81 RKACNMKKIAKICLTKYDGDIPSSLDELLALPGIGPKMANMV 122
R + + A L +Y + S E L G ++ M+
Sbjct: 34 RHTRFVFQKALRSLQRYPLPL-RSGKEAKILQHFGDRLCRML 74
>3r4i_A Citrate lyase; TIM beta/alpha-barrel, structural genomics, joint
center for structural genomics, JCSG, protein structure
initiative; 2.24A {Burkholderia xenovorans}
Length = 339
Score = 26.9 bits (60), Expect = 6.7
Identities = 5/25 (20%), Positives = 7/25 (28%), Gaps = 6/25 (24%)
Query: 165 REALQRWL------PKEEWVRINPL 183
E + L VRI+
Sbjct: 67 AELVASLLGSEHDRFGRVGVRIHDF 91
>2yxh_A MAZG-related protein; TM0360, LEFT-handed superhelix fold,
structural genomics; 2.00A {Thermotoga maritima}
Length = 116
Score = 25.6 bits (57), Expect = 7.0
Identities = 10/30 (33%), Positives = 14/30 (46%), Gaps = 4/30 (13%)
Query: 58 AEAIDKADEATIK----DLIYPVAFYTRKA 83
AEA+ K D A ++ D+IY A
Sbjct: 39 AEAVKKNDLANLEEEIGDMIYDALLVAAVA 68
>3b0x_A DNA polymerase beta family (X family); structural genomics, riken
structural genomics/proteomics in RSGI, polxc, PHP, DRP
lyase; HET: DNA DGT; 1.36A {Thermus thermophilus} PDB:
3au2_A* 3au6_A* 3auo_A* 3b0y_A*
Length = 575
Score = 27.0 bits (59), Expect = 7.2
Identities = 10/40 (25%), Positives = 19/40 (47%), Gaps = 5/40 (12%)
Query: 94 LTKYDGDIPSSLDELLALPGIGPKMANMVMTLGWFNVQGI 133
+ +P + E++ +PG+GPK A + + GI
Sbjct: 81 HEELSRKVPRGVLEVMEVPGVGPKTARL-----LYEGLGI 115
>3qqw_A Putative citrate lyase; TIM beta/alpha-barrel, structural genomics,
joint center for structural genomics, JCSG, protein
structure initiative; HET: MSE; 2.44A {Ralstonia
eutropha}
Length = 332
Score = 26.5 bits (59), Expect = 7.6
Identities = 5/30 (16%), Positives = 9/30 (30%), Gaps = 2/30 (6%)
Query: 156 QKTSSPEQTREALQ--RWLPKEEWVRINPL 183
Q+ E + R + RI+
Sbjct: 63 QEREHAEMVARMIASDRNVHGRAGARIHDP 92
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
0.317 0.132 0.395
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: 3,458,377
Number of extensions: 195725
Number of successful extensions: 598
Number of sequences better than 10.0: 1
Number of HSP's gapped: 577
Number of HSP's successfully gapped: 66
Length of query: 235
Length of database: 6,701,793
Length adjustment: 91
Effective length of query: 144
Effective length of database: 4,160,982
Effective search space: 599181408
Effective search space used: 599181408
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: 56 (25.5 bits)