RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy4002
(378 letters)
>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 = 151 bits (383), Expect = 5e-44
Identities = 64/230 (27%), Positives = 110/230 (47%), Gaps = 38/230 (16%)
Query: 148 YHVLISLMLSSQTKDE-VNHAAMGRLKEHGLTIENICNTSEDVLGKLIIPVGFWKTKAKH 206
+ +LI+++LS+Q D VN RL E T + + L + I +G ++ KA++
Sbjct: 34 FELLIAVVLSAQCTDALVN-KVTKRLFEKYRTPHDYIAVPLEELEQDIRSIGLYRNKARN 92
Query: 207 IKMASDILKKNYNNDIPNTIELLCKLPGVGPKMAHLCMNHAWGIVTGIGKDESRQPILSP 266
I+ +L YN ++P + L KLPGVG K A++ ++ A+G+
Sbjct: 93 IQKLCAMLIDKYNGEVPRDRDELMKLPGVGRKTANVVVSVAFGV---------------- 136
Query: 267 SSRQISRSELICVRKCEKKIPQLCVDVHVHRISHRLGWTKVFKTPEDTRKELESWLPESL 326
P + VD HV R+S RLG+ + + + K L +P+
Sbjct: 137 --------------------PAIAVDTHVERVSKRLGFCRWDDSVLEVEKTLMKIIPKEE 176
Query: 327 WSEVNHLLVGFGQQICKSQRPSCETCLNKDLCPQGKKELAERVKKSPKKR 376
WS +H ++ FG+ CK+Q P C +C LC +GKK + +R +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 = 140 bits (355), Expect = 4e-40
Identities = 52/217 (23%), Positives = 94/217 (43%), Gaps = 39/217 (17%)
Query: 148 YHVLISLMLSSQTKDE-VNHAAMGRLKEHGLTIENICNTSEDVLGKLIIPVGFWKTKAKH 206
+ +LI+++LS+Q D VN A +L T + + + I +G + +KA++
Sbjct: 30 FELLIAVLLSAQATDVSVN-KATAKLYPVANTPAAMLELGVEGVKTYIKTIGLYNSKAEN 88
Query: 207 IKMASDILKKNYNNDIPNTIELLCKLPGVGPKMAHLCMNHAWGIVTGIGKDESRQPILSP 266
I IL + +N ++P L LPGVG K A++ +N A+G
Sbjct: 89 IIKTCRILLEQHNGEVPEDRAALEALPGVGRKTANVVLNTAFGW---------------- 132
Query: 267 SSRQISRSELICVRKCEKKIPQLCVDVHVHRISHRLGWTKVFKTPEDTRKELESWLPESL 326
P + VD H+ R+ +R + K E ++L +P
Sbjct: 133 --------------------PTIAVDTHIFRVCNRTQFAP-GKNVEQVEEKLLKVVPAEF 171
Query: 327 WSEVNHLLVGFGQQICKSQRPSCETCLNKDLCPQGKK 363
+ +H L+ G+ C +++P C +C+ +DLC +K
Sbjct: 172 KVDCHHWLILHGRYTCIARKPRCGSCIIEDLCEYKEK 208
>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 = 129 bits (327), Expect = 5e-36
Identities = 35/230 (15%), Positives = 73/230 (31%), Gaps = 65/230 (28%)
Query: 143 PEVRRYHVLISLMLSSQTKDEVNHAAMGRLKEHGL-------TIENICNTSEDVLGKLII 195
P ++ L+ +L+ TK E ++ LK + ++ I L + +
Sbjct: 26 PNALKFEALLGAVLTQNTKFEAVLKSLENLKNAFILENDDEINLKKIAYIEFSKLAECVR 85
Query: 196 PVGFWKTKAKHIKMASDILKKNYN----NDIPNTIELLCKLPGVGPKMAHLCMNHAWGIV 251
P GF+ KAK + S + K++ T E L G+G + A + +A
Sbjct: 86 PSGFYNQKAKRLIDLSGNILKDFQSFENFKQEVTREWLLDQKGIGKESADAILCYACA-- 143
Query: 252 TGIGKDESRQPILSPSSRQISRSELICVRKCEKKIPQLCVDVHVHRISHRLGWTKVFKTP 311
+ VD + + +LG +
Sbjct: 144 ----------------------------------KEVMVVDKYSYLFLKKLGIEI--EDY 167
Query: 312 EDTRKELESWLPES----------------LWSEVNHLLVGFGQQICKSQ 345
++ + E + E+ L++ + +V F +Q + +
Sbjct: 168 DELQHFFEKGVQENLNSALALYENTISLAQLYARFHGKIVEFSKQKLELK 217
>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 = 98.1 bits (244), Expect = 3e-24
Identities = 26/214 (12%), Positives = 60/214 (28%), Gaps = 61/214 (28%)
Query: 142 APEVRRYHVLISLMLSSQTKDEVNHAAMGRLKEHGLTIENICNTSEDVLGKLIIPVG--F 199
+ E + L +L++ + + A+ L + +E+ + ++ F
Sbjct: 28 SNEEVWFRELTLCLLTANSSFISAYQALNCLGQKIYYA------NEEEIRNILKSCKYRF 81
Query: 200 WKTKAKHIKMASDILKKNYNNDIPNTI--------ELLCKLPGVGPKMAHLCMNHAWGIV 251
+ KAK+I MA + + +I E L + G+G + A + +
Sbjct: 82 YNLKAKYIIMAREKVYGRLKEEIKPLADEDQQLARERLLNIKGIGMQEASHFLRNVGYFD 141
Query: 252 TGIGKDESRQPILSPSSRQISRSELICVRKCEKKIPQLCVDVHVHRISHRLGWTKVFKTP 311
I +D H+ R+G
Sbjct: 142 LAI------------------------------------IDRHIIDFMRRIGAIGETNVK 165
Query: 312 EDTRKELESWLPESLWSEVNHLLVGFGQQICKSQ 345
+ ++ + ++L + S
Sbjct: 166 QLSKSL---------YISFENILKSIASNLNMSV 190
>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 = 90.1 bits (223), Expect = 3e-21
Identities = 36/252 (14%), Positives = 74/252 (29%), Gaps = 58/252 (23%)
Query: 100 TKKTKWEPAHWKEVLNNIREMRKHGDAPVDAMGWDHSANVDIAPEVRRYHVLISLMLSSQ 159
+ K H +E+L + +R+ V+ + + E + L +L++
Sbjct: 3 SDKIHHHHHHMEELLKELERIREEAKPLVEQRFEEFKRLGEEGTEEDLFCELSFCVLTAN 62
Query: 160 TKDEVNHAAMGRLKEHGLTIENICNTSEDVLGKLIIPVG--FWKTKAKHIKMASDI---L 214
E A + + + + L + + VG + + +A+ I + L
Sbjct: 63 WSAEGGIRAQKEIG------KGFVHLPLEELAEKLREVGHRYPQKRAEFIVENRKLLGKL 116
Query: 215 KKNYNNDIPNTIE-LLCKLPGVGPKMAHLCMNHAWGIVTGIGKDESRQPILSPSSRQISR 273
K D + E L+ G+G K A + + I
Sbjct: 117 KNLVKGDPFQSREFLVRNAKGIGWKEASHFLRNTGVEDLAI------------------- 157
Query: 274 SELICVRKCEKKIPQLCVDVHVHRISHRLGWTKVFKTPEDTRKELESWLPESLWSEVNHL 333
+D HV R+ R G + ++K + V +
Sbjct: 158 -----------------LDKHVLRLMKRHGLIQ-EIPKGWSKKR---------YLYVEEI 190
Query: 334 LVGFGQQICKSQ 345
L + +S
Sbjct: 191 LRKVAEAFGESP 202
>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 = 58.6 bits (142), Expect = 1e-10
Identities = 16/90 (17%), Positives = 37/90 (41%), Gaps = 7/90 (7%)
Query: 148 YHVLISLMLSSQTKDEVNHAAMGRLKEHGLTIENICNTSEDVLGKLIIPVGFWKTKAKHI 207
+ +LI+ + ++T ++ + + E + E + +L+ P+G + +AK I
Sbjct: 32 WKLLIATIFLNRTSGKMAIPVLWKFLEKYPSAEVARTADWRDVSELLKPLGLYDLRAKTI 91
Query: 208 KMASDILKKNYNNDIPNTIELLCKLPGVGP 237
SD + + +L G+G
Sbjct: 92 VKFSDEY-------LTKQWKYPIELHGIGK 114
>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 = 48.9 bits (116), Expect = 6e-07
Identities = 28/243 (11%), Positives = 70/243 (28%), Gaps = 59/243 (24%)
Query: 109 HWKEVLNNIREMRKHGDAPVDAMGWDHSANVDIAPEVRRYHVLISLMLSSQTKDEVNHAA 168
H ++ I E++ + + + L +L++ E
Sbjct: 6 HHMMLIKKIEELKNSEIKDIIDKRIQEFKSFKNKSNEEWFKELCFCILTANFTAEGGIRI 65
Query: 169 MGRLKEHGLTIENICNTSEDVLGKLIIPVG--FWKTKAKHIKMASDILKKNYNNDIPNTI 226
+ + + L + + +G F++ +A++I +A +
Sbjct: 66 QKEIGD------GFLTLPREELEEKLKNLGHRFYRKRAEYIVLARRFKNIKDIVESFENE 119
Query: 227 -----ELLCKLPGVGPKMAHLCMNHAWGIVTGIGKDESRQPILSPSSRQISRSELICVRK 281
L+ + G+G K A +H + +G D+
Sbjct: 120 KVAREFLVRNIKGIGYKEA----SH---FLRNVGYDDV---------------------- 150
Query: 282 CEKKIPQLCVDVHVHRISHRLGWTKVFKTPEDTRKELESWLPESLWSEVNHLLVGFGQQI 341
+D H+ R + + E+ L + E+ ++L G+++
Sbjct: 151 -------AIIDRHILRELYENNYI----------DEIPKTLSRRKYLEIENILRDIGEEV 193
Query: 342 CKS 344
Sbjct: 194 NLK 196
>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 = 50.0 bits (119), Expect = 9e-07
Identities = 41/279 (14%), Positives = 87/279 (31%), Gaps = 86/279 (30%)
Query: 21 GKQKR-MHM-------VVK--YDE--PKFQQTRCQLEKNIALNNPLDDKEHNDNKTQNKK 68
G Q++ M M + ++ F+ T +I +NNP++ H + +
Sbjct: 1625 GSQEQGMGMDLYKTSKAAQDVWNRADNHFKDTYGFSILDIVINNPVNLTIHFGGEKGKRI 1684
Query: 69 NTLYKSEKLGKRTLLKKQNVHNK-DPIPDENDTKKTKWEPAHWKEVLNN----------- 116
Y + T++ + K +E+ T T + K +L+
Sbjct: 1685 RENY--SAMIFETIVDGKLKTEKIFKEINEHSTSYT-FR--SEKGLLSATQFTQPALTLM 1739
Query: 117 ----IREMRKHGDAPVDAM--GWDHS----------ANV-DIAPEVRRYHVLI----SLM 155
+++ G P DA G HS A+V I V ++ M
Sbjct: 1740 EKAAFEDLKSKGLIPADATFAG--HSLGEYAALASLADVMSIESLVE----VVFYRGMTM 1793
Query: 156 LSSQTKDE----------VNHAAMG-RLKEHGLT--IENICNTSEDVL--------GKLI 194
+ +DE +N + + L +E + + ++ +
Sbjct: 1794 QVAVPRDELGRSNYGMIAINPGRVAASFSQEALQYVVERVGKRTGWLVEIVNYNVENQQY 1853
Query: 195 IPVGFWKTKAKHIKMASDILKKNYNNDIPNTIELLCKLP 233
+ G +A + +++L I + +L
Sbjct: 1854 VAAG--DLRA--LDTVTNVLNFIKLQKID-----IIELQ 1883
Score = 43.9 bits (103), Expect = 9e-05
Identities = 77/473 (16%), Positives = 134/473 (28%), Gaps = 178/473 (37%)
Query: 10 TLTVPVDTTKNGKQKRMHMVVKYDEPKFQQTRCQLEKNIALNN-PLDDKE-------HND 61
L VP + Q + ++ F + + + A ++ P E +
Sbjct: 19 VLLVPTASFFIASQLQ-------EQ--FNKILPEPTEGFAADDEPTTPAELVGKFLGYVS 69
Query: 62 NKTQNKKNTLYKSEKLG------KRTLLKKQNVHN-KDPIPDENDTKKTKWEPAHWKEVL 114
+ + K + + L + L+ ++H + ENDT K KE++
Sbjct: 70 SLVEPSKVGQF-DQVLNLCLTEFENCYLEGNDIHALAAKLLQENDTTLVKT-----KELI 123
Query: 115 NNIREMRKHGDAPVDAMGWDHSANVDIAPEVRRYHVLISLMLSSQTKDEVNHAAMG---- 170
N R P D +SA L + + A G
Sbjct: 124 KNYITARIMAKRPFDKKS--NSA----------------LFRAVGEGNAQLVAIFGGQGN 165
Query: 171 ---RLKE--------HGLTIENICNTSEDVLGKL---------IIPVGF----WKTKAKH 206
+E H L + ++ S + L +L + G W
Sbjct: 166 TDDYFEELRDLYQTYHVL-VGDLIKFSAETLSELIRTTLDAEKVFTQGLNILEW------ 218
Query: 207 IKMASDILKKNYNNDIP---NTIELL--------CKLPGVGPK--MAHLC--MNHAWGIV 251
++ S+ K+Y IP I ++ KL G P ++L H+ G+V
Sbjct: 219 LENPSNTPDKDYLLSIPISCPLIGVIQLAHYVVTAKLLGFTPGELRSYLKGATGHSQGLV 278
Query: 252 TG-------------------------IGKDESRQ--PILS----------------PSS 268
T IG + P S PS
Sbjct: 279 TAVAIAETDSWESFFVSVRKAITVLFFIGV-RCYEAYPNTSLPPSILEDSLENNEGVPSP 337
Query: 269 ----RQISRSELIC-VRKCEKKIPQLCVDVHVHRISHRLGWTKVFKTPEDTRKELESWLP 323
+++ ++ V K +P V IS + + + S P
Sbjct: 338 MLSISNLTQEQVQDYVNKTNSHLPA---GKQVE-IS-------LVNGA---KNLVVSGPP 383
Query: 324 ESLWSEVNHLLVGFGQQICKSQRPSCETCLNKDLCPQGKKELAERVKKSPKKR 376
+SL+ L K++ PS D Q + +ER K R
Sbjct: 384 QSLYGLNLTLR--------KAKAPS-----GLD---QSRIPFSER-KLKFSNR 419
Score = 42.0 bits (98), Expect = 3e-04
Identities = 38/265 (14%), Positives = 73/265 (27%), Gaps = 100/265 (37%)
Query: 16 DTTKNGKQKRMHM-VVKYDEPKFQQTRCQLEKNI-ALNNPLDDKEH------NDNKTQNK 67
D+ +N + M + + + Q++ + N+ L + N
Sbjct: 326 DSLENNEGVPSPMLSIS-NLT-----QEQVQDYVNKTNSHLPAGKQVEISLVN-----GA 374
Query: 68 KN--------TLYKSEKLGKRTLLKKQNVHNKDPIPDENDTKKTKWEPAHWKEVLNNIRE 119
KN +LY G L+K P D + + E
Sbjct: 375 KNLVVSGPPQSLY-----GLNLTLRKAKA------PSGLDQSRIPF------------SE 411
Query: 120 MRKHGDA---PVDAMGWDHSANVDIAPEVRRYHVLISLMLSSQTKDEVNHAAMGRLKEHG 176
+ PV +P +H S +L + L ++
Sbjct: 412 RKLKFSNRFLPVA------------SP----FH---SHLLV-----PASDLINKDLVKNN 447
Query: 177 LTIENICNTSEDVLGKLIIPVGFWKTKAKHIKMASDILKKNYNNDIPNTIELLCKLPGVG 236
++ ++D + IPV SD L+ + ++ + +LP V
Sbjct: 448 VSFN-----AKD----IQIPV-------YDTFDGSD-LRVLSGSISERIVDCIIRLP-VK 489
Query: 237 -PKMAHLCMNHAW----GIVTGIGK 256
H G +G+G
Sbjct: 490 WETTTQFKATHILDFGPGGASGLGV 514
>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 = 40.6 bits (94), Expect = 7e-04
Identities = 51/453 (11%), Positives = 117/453 (25%), Gaps = 144/453 (31%)
Query: 15 VDTTKNGKQKRMHMVVKYDEPKFQQT-RCQ----LEKNIALNNPLDD---KEHNDNKT-- 64
+D Q + ++ E F C+ + K+I +D + + T
Sbjct: 7 MDFETGEHQYQYKDILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTLR 66
Query: 65 -----QNKKNTLYK---SEKLGK--RTLLKKQNVHNKDPIPDE-----------ND---- 99
+K+ + + E L + L+ + P ND
Sbjct: 67 LFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVF 126
Query: 100 TKKTKWEPAHWKEVLNNIREMRKHGDAPVDAMG-----WDHSANVDIAPEVRRYHVLISL 154
K + ++ + E+R + +D + W +A +V + +
Sbjct: 127 AKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTW-------VALDVCLSYKVQCK 179
Query: 155 MLSSQTKDEVNHAAMGRLKEHGLTIE---NIC-------NTSEDVLGKLIIPVGFWKTKA 204
M ++ + +E + + D + + + + +
Sbjct: 180 M-----DFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAEL 234
Query: 205 KHIKMASDILKKNYNN------DI--PNTIELL---CKL------PGV-----GPKMAHL 242
+ + + K Y N ++ CK+ V H+
Sbjct: 235 RRL-----LKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHI 289
Query: 243 CMNHAWGIVTGIGKDESRQPILSPSSRQISRSEL---ICVRKCEKKIPQLC------VDV 293
++H + DE + +L +L + P+ +
Sbjct: 290 SLDH---HSMTLTPDEVKS-LLL-KYLDCRPQDLPREVL-----TTNPRRLSIIAESIRD 339
Query: 294 HVHRISHRLGWTKVFK--------------TPEDTRKELES--------WLPES----LW 327
+ + W V P + RK + +P +W
Sbjct: 340 GLATWDN---WKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIW 396
Query: 328 SEVNHLLVGFGQQI-CKSQRPSCETCLNKDLCP 359
+V V + K + S + K
Sbjct: 397 FDVIKSDV---MVVVNKLHKYS---LVEKQPKE 423
Score = 29.4 bits (65), Expect = 2.5
Identities = 37/217 (17%), Positives = 67/217 (30%), Gaps = 54/217 (24%)
Query: 75 EKLGKRTLLKKQNVHNKDPIPDENDTKKTKWEPAHWKEVLNNIREMRKHGDAPVDAMGWD 134
KL K +L++KQ + IP K K L N +
Sbjct: 409 NKLHKYSLVEKQPKESTISIPSIYLELKVK---------LENEYAL-------------- 445
Query: 135 HSANVDIAPEVRRYHVLISLMLSSQTKDEV-----NHAAMGRLKEHGLTIENICNTSEDV 189
H + VD Y++ + + +H +G H IE+ +
Sbjct: 446 HRSIVD------HYNIPKTFDSDDLIPPYLDQYFYSH--IGH---HLKNIEHP--ERMTL 492
Query: 190 LGKLIIPVGFWKTKAKHIKMA-------SDILK--KNYNNDI----PNTIELLCKLPGVG 236
+ + F + K +H A + L+ K Y I P L+ +
Sbjct: 493 FRMVFLDFRFLEQKIRHDSTAWNASGSILNTLQQLKFYKPYICDNDPKYERLVNAILDFL 552
Query: 237 PKMAHLCMNHAWGIVTGIGKDESRQPILSPSSRQISR 273
PK+ + + + I + I + +Q+ R
Sbjct: 553 PKIEENLICSKYTDLLRIALMAEDEAIFEEAHKQVQR 589
>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 = 39.1 bits (92), Expect = 0.001
Identities = 40/230 (17%), Positives = 73/230 (31%), Gaps = 71/230 (30%)
Query: 148 YHVLIS-LMLSSQTKDEVNHAA------MGRLKEHGLTIENICNTSEDVLGKLIIPVGFW 200
Y +LI+ ++L +T H + K E+I T + + K I +G
Sbjct: 36 YVILITEILLR-RTT--AGHVKKIYDKFFVKYK----CFEDILKTPKSEIAKDIKEIGLS 88
Query: 201 KTKAKHIKMASDILKKNYNNDIPNTIELLCKLPGVGPKMAHLCMNHAWGIVTGIGKDESR 260
+A+ +K + ++ +Y +P + + LPGVG V + + +
Sbjct: 89 NQRAEQLKELARVVINDYGGRVPRNRKAILDLPGVGKYTC--------AAVMCLAFGK-K 139
Query: 261 QPILSPSSRQISRSELICVRKCEKKIPQLCVDVHVHRISHRLGWTKVFKTPEDTRKELES 320
+ VD + R+ +R F +
Sbjct: 140 AAM---------------------------VDANFVRVINRY-----FGGSYENLNYNH- 166
Query: 321 WLPESLWSEVNHLL----VG--------FGQQICKSQRPSCETCLNKDLC 358
++LW L+ F IC ++P CE C LC
Sbjct: 167 ---KALWELAETLVPGGKCRDFNLGLMDFSAIICAPRKPKCEKCGMSKLC 213
>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 = 36.3 bits (84), Expect = 0.011
Identities = 17/155 (10%), Positives = 36/155 (23%), Gaps = 29/155 (18%)
Query: 107 PAHWKEVLNNIREMRKHGDAPVDAMGWDHSANVDIAPEVRR------YHVLISLMLSSQT 160
E L + + + P +R + + +L
Sbjct: 68 EPVAAECLAKMSRLF-DLQCNPQIVNGALGRLGAARPGLRLPGCVDAFEQGVRAILGQLV 126
Query: 161 KDEVNHAAMGRLKEH-------------GLTIENICNTSEDVLGKLIIPVGFWKTKAKHI 207
+ R+ + T + + L L G +A+ +
Sbjct: 127 SVAMAAKLTARVAQLYGERLDDFPEYICFPTPQRLAAADPQALKAL----GMPLKRAEAL 182
Query: 208 K-----MASDILKKNYNNDIPNTIELLCKLPGVGP 237
L D+ ++ L PG+G
Sbjct: 183 IHLANAALEGTLPMTIPGDVEQAMKTLQTFPGIGR 217
>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 = 36.4 bits (84), Expect = 0.011
Identities = 26/197 (13%), Positives = 53/197 (26%), Gaps = 61/197 (30%)
Query: 148 YHVLISLMLSSQTKDEVNHAAMGRLKEHG--------------LTIENICNTSEDVLGKL 193
+ +L+S ++S+ + + + + E T++ + +E +
Sbjct: 116 FEILLSFIISANNRIPMIKKCINNISEKAGKKLEYKGKIYYAFPTVDKLHEFTEKDFEEC 175
Query: 194 IIPVGFWKTKAKHIKMASDILKKNYNN-------DIPNTIELLCKLPGVGPKMAHLCMNH 246
+AK++K D + N + E L K GVGP++A M
Sbjct: 176 TAG-----FRAKYLKDTVDRIYNGELNLEYIKSLNDNECHEELKKFMGVGPQVADCIMLF 230
Query: 247 AWGIVTGIGKDESRQPILSPSSRQISRSELICVRKCEKKIPQLCVDVHVHRISHRLGWTK 306
+ + P VD V + L
Sbjct: 231 SMQ-----------------------KYSA---------FP---VDTWVKKAMMSLYVAP 255
Query: 307 VFKTPEDTRKELESWLP 323
+ E +
Sbjct: 256 DVSLKKIRDFGREKFGS 272
>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 = 36.1 bits (84), Expect = 0.013
Identities = 34/180 (18%), Positives = 56/180 (31%), Gaps = 42/180 (23%)
Query: 204 AKHIKMASDILKKNYNNDIPNTIELLCKLPGVGPKMAHLCMNHAWGIVTGIGKDESRQPI 263
+++ A +K Y +P+ + +L GVGP G V + +P
Sbjct: 95 VRNLHAAVKEVKTRYGGKVPDDPDEFSRLKGVGPYTV--------GAVLSLAYGV-PEPA 145
Query: 264 LSPSSRQISRSELICVRKCEKKIPQLCVDVHVHRISHRL----GWTKVFKTPEDTRKELE 319
VD +V R+ RL T + + +
Sbjct: 146 ---------------------------VDGNVMRVLSRLFLVTDDIAKPSTRKRFEQIVR 178
Query: 320 SWLPESLWSEVNHLLVGFGQQICKSQRPSCETCLNKDLCPQGKKELAER--VKKSPKKRK 377
+ N L+ G +C +RPSC C + C + +AE VK K
Sbjct: 179 EIMAYENPGAFNEALIELGALVCTPRRPSCLLCPVQAYCQAFAEGVAEELPVKMKKTAVK 238
>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 = 34.4 bits (80), Expect = 0.036
Identities = 29/164 (17%), Positives = 49/164 (29%), Gaps = 50/164 (30%)
Query: 204 AKHIKMASDILKKNYNNDIPNTIELLCKLPGVGPKMAHLCMNHAWGIVTGIGKDESRQPI 263
A+++ A+ + + P T E + LPGVG A G + + + PI
Sbjct: 86 ARNLHKAAQQVATLHGGKFPETFEEVAALPGVGRSTA--------GAILSLSLGK-HFPI 136
Query: 264 LSPSSRQISRSELICVRKCEKKIPQLCVDVHVHRISHRLGWTKVFKTPED-----TRKEL 318
+D +V R+ R + +L
Sbjct: 137 ---------------------------LDGNVKRVLARC-----YAVSGWPGKKEVENKL 164
Query: 319 ----ESWLPESLWSEVNHLLVGFGQQICKSQRPSCETCLNKDLC 358
E P N ++ G IC +P C C ++ C
Sbjct: 165 WSLSEQVTPAVGVERFNQAMMDLGAMICTRSKPKCSLCPLQNGC 208
>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 = 34.8 bits (80), Expect = 0.041
Identities = 15/69 (21%), Positives = 24/69 (34%), Gaps = 12/69 (17%)
Query: 178 TIENICNTSEDVLGKLIIPVGFWKTKAKHIKMASDILKKNYNNDIPN-----TIELLCKL 232
T E I + L + G + KA+ I +I K+ ++ E L
Sbjct: 163 TQEAILKAGVEGLREC----GLSRRKAELIV---EIAKEENLEELKEWGEEEAYEYLTSF 215
Query: 233 PGVGPKMAH 241
G+G A
Sbjct: 216 KGIGRWTAE 224
>4ecq_A DNA polymerase ETA; transferase-DNA complex; HET: DNA DTP; 1.50A
{Homo sapiens} PDB: 3mr2_A* 3mr4_A* 3mr5_A* 3si8_A*
4dl2_A* 4dl3_A* 4dl4_A* 4dl5_A* 4dl6_A* 4dl7_A* 3mr3_A*
4ecr_A* 4ecs_A* 4ect_A* 4ecu_A* 4ecv_A* 4ecw_A* 4ecx_A*
4ecy_A* 4ecz_A* ...
Length = 435
Score = 34.6 bits (79), Expect = 0.054
Identities = 27/177 (15%), Positives = 51/177 (28%), Gaps = 47/177 (26%)
Query: 208 KMASDILKKN-----YNNDIPNTIELLC--KLPGVGPKMAHLCMNHAWGIVTGIGKDESR 260
K+A + K N + +P + K+ +G K+ + GI +
Sbjct: 227 KLACGLNKPNRQTLVSHGSVPQLFSQMPIRKIRSLGGKLGASVI-EILGIEY--MGE--- 280
Query: 261 QPILSPSSRQISRSELICVRKCEKKIPQLCVDVHVHRISHRLGWTKVFKTPEDTRKELES 320
Q + S+L +K ++ + + V P K
Sbjct: 281 -------LTQFTESQLQ--SHFGEKNGS-----WLYAMCRGIEHDPV--KPRQLPK---- 320
Query: 321 WLPESLWSEVNHLLVGFGQQICKSQRPSCETCLNKDLCPQGKKELAERVKKSPKKRK 377
++ N F + + R + L L +EL ER+ K
Sbjct: 321 ----TIGCSKN-----FPGKTALATREQVQWWL-LQLA----QELEERLTKDRNDND 363
>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 = 33.9 bits (77), Expect = 0.077
Identities = 16/127 (12%), Positives = 36/127 (28%), Gaps = 29/127 (22%)
Query: 148 YHVLISLMLSSQTKDEVNHAAMGRLKEH---------------GLTIENICNTSEDVLGK 192
L S + SS + RL + +++ + + +
Sbjct: 153 IECLFSFICSSNNNIARITGMVERLCQAFGPRLIQLDDVTYHGFPSLQALAGPEVEAHLR 212
Query: 193 LIIPVGFWKTKAKHIKMASDILKKNYNN----------DIPNTIELLCKLPGVGPKMAHL 242
+ +A+++ ++ + + + LC LPGVG +A
Sbjct: 213 KL----GLGYRARYVSASARAILEEQGGLAWLQQLRESSYEEAHKALCILPGVGTCVADK 268
Query: 243 CMNHAWG 249
A
Sbjct: 269 ICLMALD 275
>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 = 32.6 bits (75), Expect = 0.14
Identities = 10/24 (41%), Positives = 14/24 (58%)
Query: 217 NYNNDIPNTIELLCKLPGVGPKMA 240
Y + + I L +LPG+GPK A
Sbjct: 2 KYPPSLVSLIRELSRLPGIGPKSA 25
>2yg9_A DNA-3-methyladenine glycosidase II, putative; hydrolase, DNA
repair; 1.95A {Deinococcus radiodurans} PDB: 2yg8_A
Length = 225
Score = 31.9 bits (73), Expect = 0.22
Identities = 17/80 (21%), Positives = 30/80 (37%), Gaps = 13/80 (16%)
Query: 167 AAMGRLKEH--GLTIENICNTSEDVLGKLIIPVGFWKTKAKHIK-MASDILKKNYN-NDI 222
A GRL+ G+ + S D L + G K + ++ A+ + + +
Sbjct: 81 AIYGRLEGLPGGVVPAALLKVSGDDLRGV----GLSWAKVRTVQAAAAAAVSGQIDFAHL 136
Query: 223 PN-----TIELLCKLPGVGP 237
I L +LPG+G
Sbjct: 137 SGQPDELVIAELVQLPGIGR 156
>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 = 31.6 bits (72), Expect = 0.31
Identities = 12/74 (16%), Positives = 27/74 (36%), Gaps = 11/74 (14%)
Query: 171 RLKEHGLTIENICNTSEDVLGKLIIPVGFWKTKAKHIK-MASDILKKNYN-NDIPNT--- 225
+ E + S++ L + G K K ++I+ + + + ++
Sbjct: 79 LVGGALEKPEQLYRVSDEALRQA----GVSKRKIEYIRHVCEHVESGRLDFTELEGAEAT 134
Query: 226 --IELLCKLPGVGP 237
IE L + G+G
Sbjct: 135 TVIEKLTAIKGIGQ 148
>1jx4_A DNA polymerase IV (family Y); protein-DNA complex, Y-family,
transferase-D complex; HET: DNA MSE ADI; 1.70A
{Sulfolobus solfataricus} SCOP: d.240.1.1 e.8.1.7 PDB:
1jxl_A* 1n48_A* 1n56_A* 1ryr_A* 1rys_A* 1s0m_A* 1s0n_A*
1s0o_A* 1s10_A* 1s97_A* 1s9f_A* 2ia6_A* 2ibk_A* 2r8g_A*
2r8h_A* 2r8i_A* 2rdj_A* 3fds_A* 3m9m_B* 3m9n_B* ...
Length = 352
Score = 31.0 bits (71), Expect = 0.62
Identities = 14/54 (25%), Positives = 22/54 (40%), Gaps = 11/54 (20%)
Query: 208 KMASDILKKN-----YNNDIPNTIELL--CKLPGVGPKMA-HLCMNHAWGIVTG 253
K+A+D+ K N + ++ I L +PG+G A L GI
Sbjct: 152 KIAADMAKPNGIKVIDDEEVKRLIRELDIADVPGIGNITAEKL---KKLGINKL 202
>3bq0_A POL IV, DBH, DNA polymerase IV; Y-family, lesion bypass; HET: DNA;
2.60A {Sulfolobus acidocaldarius} SCOP: d.240.1.1
e.8.1.7 PDB: 3bq1_A* 3bq2_A* 1k1q_A 1k1s_A
Length = 354
Score = 31.0 bits (71), Expect = 0.66
Identities = 12/54 (22%), Positives = 23/54 (42%), Gaps = 11/54 (20%)
Query: 208 KMASDILKKN-----YNNDIPNTIELL--CKLPGVGPKMA-HLCMNHAWGIVTG 253
K+ +D K N ++ + + L ++PG+G +A L + GI
Sbjct: 153 KIIADKSKPNGLGVIRPTEVQDFLNELDIDEIPGIGSVLARRL---NELGIQKL 203
>1im4_A DBH; DNA polymerase PALM, thumb, fingers, helix-hairpin-helix,
fidelity, processivity, transferase; 2.30A {Sulfolobus
solfataricus} SCOP: e.8.1.7
Length = 221
Score = 30.2 bits (69), Expect = 0.85
Identities = 12/54 (22%), Positives = 23/54 (42%), Gaps = 11/54 (20%)
Query: 208 KMASDILKKN-----YNNDIPNTIELL--CKLPGVGPKMA-HLCMNHAWGIVTG 253
K+ +D K N ++ + + L ++PG+G +A L + GI
Sbjct: 158 KIIADKSKPNGLGVIRPTEVQDFLNELDIDEIPGIGSVLARRL---NELGIQKL 208
>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 = 30.7 bits (69), Expect = 0.87
Identities = 14/55 (25%), Positives = 22/55 (40%), Gaps = 11/55 (20%)
Query: 208 KMASDILKKN-------YNNDIPNTIELL--CKLPGVGPKMAHLCMNHAWGIVTG 253
K+ SD K N + + I+ L K+ G+G + A GI+T
Sbjct: 254 KVCSDKNKPNGQYQILPNRQAVMDFIKDLPIRKVSGIGKVTEKML--KALGIITC 306
>3gqc_A DNA repair protein REV1; protein-DNA complex, DNA damage, DNA
repair, DNA synthesis, binding, magnesium,
metal-binding; HET: DNA DOC DCP; 2.50A {Homo sapiens}
Length = 504
Score = 30.6 bits (69), Expect = 0.98
Identities = 14/54 (25%), Positives = 21/54 (38%), Gaps = 11/54 (20%)
Query: 208 KMASDILKKN-----YNNDIPNTIELL--CKLPGVGPKMAH-LCMNHAWGIVTG 253
+MA+ K + ++ + I LPGVG M L + GI T
Sbjct: 289 RMATRKAKPDGQYHLKPEEVDDFIRGQLVTNLPGVGHSMESKL---ASLGIKTC 339
>4e69_A 2-dehydro-3-deoxygluconokinase; putative sugar kinase, enzyme
function initiative, EFI, STRU genomics, transferase;
1.60A {Oceanicola granulosus} PDB: 4ebu_A* 4eum_A*
Length = 328
Score = 30.3 bits (69), Expect = 0.98
Identities = 10/61 (16%), Positives = 18/61 (29%), Gaps = 3/61 (4%)
Query: 120 MRKHGDAPVDAMGWDHSANVDIAPEVRRYHV-LISLMLSSQTKDEVNHAAMGRLKEHGLT 178
R + + D A + I+L + Q A+ + + G T
Sbjct: 123 WRG--QSAARELAGDADALAAAMARADVVYFSGITLAILDQCGRATLLRALAQARATGRT 180
Query: 179 I 179
I
Sbjct: 181 I 181
>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 = 30.0 bits (67), Expect = 1.5
Identities = 14/55 (25%), Positives = 22/55 (40%), Gaps = 11/55 (20%)
Query: 208 KMASDILKKN-------YNNDIPNTIELL--CKLPGVGPKMAHLCMNHAWGIVTG 253
K+ SD K N + + I+ L K+ G+G + A GI+T
Sbjct: 310 KVCSDKNKPNGQYQILPNRQAVMDFIKDLPIRKVSGIGKVTEKML--KALGIITC 362
>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 = 27.7 bits (62), Expect = 1.6
Identities = 8/16 (50%), Positives = 12/16 (75%)
Query: 225 TIELLCKLPGVGPKMA 240
++E L LPG+GP +A
Sbjct: 25 SLEELMALPGIGPVLA 40
>1un8_A Dihydroxyacetone kinase; transferase; HET: MYY; 2.5A {Citrobacter
freundii} SCOP: a.208.1.1 c.119.1.2 PDB: 1un9_A*
Length = 552
Score = 29.6 bits (67), Expect = 2.0
Identities = 11/78 (14%), Positives = 16/78 (20%), Gaps = 14/78 (17%)
Query: 119 EMRKHGDAPVDAMGWDHSANVDIAPEVRRYHVLISLMLSSQTKDEVNHAAMGRLKEHGLT 178
+ K V+ W V H + V
Sbjct: 313 SIEKALLTEVETSNWPTPVPPREITCVVSSHASARVEFQPSANALVAGI----------- 361
Query: 179 IENICNT---SEDVLGKL 193
+E + T E L L
Sbjct: 362 VELVTATLSDLETHLNAL 379
>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 = 29.3 bits (66), Expect = 2.2
Identities = 14/54 (25%), Positives = 21/54 (38%), Gaps = 10/54 (18%)
Query: 208 KMASDILKKN-----YNNDIPNTIELL---CKLPGVGPKMAHLCMNHAWGIVTG 253
K+ S + K N + I L ++PG+G K A A GI +
Sbjct: 207 KLVSGVFKPNQQTVLLPESCQHLIHSLNHIKEIPGIGYKTAKCL--EALGINSV 258
>1ixr_A Holliday junction DNA helicase RUVA; heterooligomeric complex,
octameric RUVA, AAA-ATPase domain, complex with
nucleotide, hydrolase; HET: ANP; 3.30A {Thermus
thermophilus} SCOP: a.60.2.1 b.40.4.2
Length = 191
Score = 28.7 bits (65), Expect = 2.2
Identities = 6/15 (40%), Positives = 8/15 (53%)
Query: 226 IELLCKLPGVGPKMA 240
LL GVG ++A
Sbjct: 106 ARLLTSASGVGRRLA 120
>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 = 27.1 bits (60), Expect = 3.2
Identities = 6/16 (37%), Positives = 8/16 (50%)
Query: 225 TIELLCKLPGVGPKMA 240
+ L L +GPK A
Sbjct: 38 SARDLRSLQRIGPKKA 53
>1cuk_A RUVA protein; DNA repair, SOS response, DNA-binding, DNA
recombination; 1.90A {Escherichia coli} SCOP: a.5.1.1
a.60.2.1 b.40.4.2 PDB: 1hjp_A 1bdx_A* 1c7y_A 1d8l_A
Length = 203
Score = 28.4 bits (64), Expect = 3.2
Identities = 8/15 (53%), Positives = 10/15 (66%)
Query: 226 IELLCKLPGVGPKMA 240
+ L KLPG+G K A
Sbjct: 107 VGALVKLPGIGKKTA 121
>3quf_A Extracellular solute-binding protein, family 1; structural
genomics, PSI-biology, midwest center for structu
genomics, MCSG; HET: MSE; 1.70A {Bifidobacterium longum
subsp}
Length = 414
Score = 28.6 bits (64), Expect = 3.2
Identities = 7/45 (15%), Positives = 13/45 (28%), Gaps = 1/45 (2%)
Query: 96 DENDTKKTKWEPAHWKEVLNNIREMRKHGDAPVDAMGWDHSANVD 140
+ + K+ + W V K G P ++G
Sbjct: 209 ADIWSGKSTFTKD-WTPVFKRWEAAAKAGVIPQKSVGLSADQVKQ 252
>2ztd_A Holliday junction ATP-dependent DNA helicase RUVA; recombination,
branch migration, DNA BIND oligomerization, acidic PIN;
2.40A {Mycobacterium tuberculosis} PDB: 2ztc_A 2zte_A
2h5x_A 1bvs_A
Length = 212
Score = 28.4 bits (64), Expect = 3.4
Identities = 5/15 (33%), Positives = 10/15 (66%)
Query: 226 IELLCKLPGVGPKMA 240
+ L ++PG+G + A
Sbjct: 122 VAALTRVPGIGKRGA 136
>2a3n_A Putative glucosamine-fructose-6-phosphate aminotr; structural
genomics, joint center for structural genomics; HET:
MSE; 1.23A {Salmonella typhimurium}
Length = 355
Score = 28.7 bits (65), Expect = 3.5
Identities = 14/77 (18%), Positives = 30/77 (38%), Gaps = 15/77 (19%)
Query: 139 VDIAPEVR-RYHVLIS----LMLSSQ---TKDEVNHAAMGRLKEHGLTIENICNTSEDVL 190
V+ A E+ + + ++ ++ S+ TK+ V A K G+ + I ++ L
Sbjct: 86 VEQAAELIHKGNKRLNKDSVVITLSKSGDTKESV--AIAEWCKAQGIRVVAITKNADSPL 143
Query: 191 GKL---IIPVGFWKTKA 204
+ IP+
Sbjct: 144 AQAATWHIPMRH--KNG 158
>2b3f_A Glucose-binding protein; protein-carbohydrate complex, periplasmic
binding protein, galactose, GBP, sugar binding protein;
HET: GAL; 1.56A {Thermus thermophilus HB27} PDB: 2b3b_A*
Length = 400
Score = 27.8 bits (62), Expect = 6.3
Identities = 3/37 (8%), Positives = 9/37 (24%)
Query: 102 KTKWEPAHWKEVLNNIREMRKHGDAPVDAMGWDHSAN 138
K K+ + + + W + +
Sbjct: 193 KLKFTDPKAVRAWEVFGRVLDCANKDAAGLSWQQAVD 229
>2a1j_A DNA repair endonuclease XPF; XPF, xeroderma pigmentosum, DNA
repair, endonuclease, helix-hairpin-helix, DNA binding
protein; HET: DNA; 2.70A {Homo sapiens} SCOP: a.60.2.5
PDB: 2kn7_A*
Length = 63
Score = 25.4 bits (56), Expect = 6.8
Identities = 8/21 (38%), Positives = 11/21 (52%)
Query: 226 IELLCKLPGVGPKMAHLCMNH 246
+ L K+PGV K M+H
Sbjct: 3 QDFLLKMPGVNAKNCRSLMHH 23
>2aq4_A DNA repair protein REV1; polymerase, PAD, N-digit, G-loop,
transferase; HET: DNA DOC DCP; 2.32A {Saccharomyces
cerevisiae} PDB: 3bjy_A* 3osp_A*
Length = 434
Score = 27.7 bits (62), Expect = 7.6
Identities = 9/54 (16%), Positives = 15/54 (27%), Gaps = 8/54 (14%)
Query: 208 KMASDILKKN------YNNDIPNTIELLC--KLPGVGPKMAHLCMNHAWGIVTG 253
++A + K N +N LPGVG + +
Sbjct: 214 RLALKMAKPNGYNITFKSNLSEEFWSSFKLDDLPGVGHSTLSRLESTFDSPHSL 267
>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 = 27.3 bits (61), Expect = 8.3
Identities = 28/180 (15%), Positives = 53/180 (29%), Gaps = 42/180 (23%)
Query: 204 AKHIKMASDILKKNYNNDIPNTIE-LLCKLPGVGPKMAHLCMNHAWGIVTGIGKDESRQP 262
+ ++ + + + +P T E L LPGVG A G + I +
Sbjct: 105 GRRLQEGARKVVEELGGHMPRTAETLQQLLPGVGRYTA--------GAIASIAFGQ-ATG 155
Query: 263 ILSPSSRQISRSELICVRKCEKKIPQLCVDVHVHRISHRL----GWTKVFKTPEDTRKEL 318
+ VD +V R+ R+ +
Sbjct: 156 V---------------------------VDGNVARVLCRVRAIGADPSSTLVSQQLWGLA 188
Query: 319 ESWLPESLWSEVNHLLVGFGQQICKSQRPSCETCLNKDLCPQGKKELAERV-KKSPKKRK 377
+ + + + N + G +C QRP C C + LC ++ E++
Sbjct: 189 QQLVDPARPGDFNQAAMELGATVCTPQRPLCSQCPVESLCRARQRVEQEQLLASGSLSGS 248
>1uf3_A Hypothetical protein TT1561; metallo-dependent phosphatases,
structural genomics, riken structural
genomics/proteomics initiative, RSGI; 2.10A {Thermus
thermophilus} SCOP: d.159.1.6
Length = 228
Score = 27.0 bits (59), Expect = 8.3
Identities = 5/25 (20%), Positives = 9/25 (36%)
Query: 283 EKKIPQLCVDVHVHRISHRLGWTKV 307
+ P L + + LG + V
Sbjct: 177 KTHNPLLVLVAGKGQKHEMLGASWV 201
>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 = 27.0 bits (60), Expect = 8.7
Identities = 15/76 (19%), Positives = 25/76 (32%), Gaps = 18/76 (23%)
Query: 173 KEHGLTIENICNTSEDVLGKLIIPVGFWKTKAKHIKMASDILKKNYNNDIPNT------- 225
T E I + +++ GF K +K I + + IP
Sbjct: 81 NGQFPTPEEIRDMDFEIMRAC----GFSARKIDSLK---SIAEATISGLIPTKEEAERLS 133
Query: 226 ----IELLCKLPGVGP 237
IE L ++ G+G
Sbjct: 134 NEELIERLTQIKGIGR 149
>1wwk_A Phosphoglycerate dehydrogenase; riken structural
genomics/proteomics initiative, RSGI, structural
genomics, oxidoreductase; HET: NAD; 1.90A {Pyrococcus
horikoshii}
Length = 307
Score = 27.1 bits (61), Expect = 9.4
Identities = 12/49 (24%), Positives = 22/49 (44%), Gaps = 8/49 (16%)
Query: 146 RRYHVLISLMLSSQTKDEVNHAAMGRLKEHGLTIENICNTSEDVLGKLI 194
+R VL++ ++ A+ LK+ GL + ED L +L+
Sbjct: 2 KRMKVLVA--------APLHEKAIQVLKDAGLEVIYEEYPDEDRLVELV 42
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
0.315 0.131 0.400
Gapped
Lambda K H
0.267 0.0562 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 5,617,503
Number of extensions: 324364
Number of successful extensions: 897
Number of sequences better than 10.0: 1
Number of HSP's gapped: 877
Number of HSP's successfully gapped: 64
Length of query: 378
Length of database: 6,701,793
Length adjustment: 95
Effective length of query: 283
Effective length of database: 4,049,298
Effective search space: 1145951334
Effective search space used: 1145951334
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 (21.6 bits)
S2: 58 (26.5 bits)