RPS-BLAST 2.2.22 [Sep-27-2009] Database: pdb70 24,244 sequences; 5,693,230 total letters Searching..................................................done Query= gi|254780845|ref|YP_003065258.1| ribonucleotide-diphosphate reductase subunit beta [Candidatus Liberibacter asiaticus str. psy62] (352 letters) >1syy_A Ribonucleoside-diphosphate reductase beta chain; DIIRON, oxygen activation, iron coupled radical, immune evasion, replication; 1.70A {Chlamydia trachomatis} SCOP: a.25.1.2 PDB: 2ani_A Length = 346 Score = 317 bits (812), Expect = 3e-87 Identities = 193/343 (56%), Positives = 258/343 (75%), Gaps = 3/343 (0%) Query: 10 IQAGEKRVNVDDKRMLNA-RSDVNQLLPLKYGWAWEKYLSACNNHWMPTEVPMQDDLALW 68 + +KRVN++ KR++N + DVNQL+P+KY WAWE YL+ C N+W+PTE+PM D+ LW Sbjct: 6 LDGKQKRVNLNSKRLVNCNQVDVNQLVPIKYKWAWEHYLNGCANNWLPTEIPMGKDIELW 65 Query: 69 KSKNGLTDDERLMIKRNLGFFASSESLVANNIVLAIYRHLSNPECRQYLLRQAFEEAVHS 128 KS + L++DER +I NLGFF+++ESLV NNIVLAI++H++NPE RQYLLRQAFEEAVH+ Sbjct: 66 KS-DRLSEDERRVILLNLGFFSTAESLVGNNIVLAIFKHVTNPEARQYLLRQAFEEAVHT 124 Query: 129 HTFQYIITSLGLDEGELFNMYREVPSITAKANWALQYTQTLSSPSFTTGTKDADQEFLQD 188 HTF YI SLGLDE E+FN Y E +I AK ++ ++ T + P+F T + + QEF+++ Sbjct: 125 HTFLYICESLGLDEKEIFNAYNERAAIKAKDDFQMEITGKVLDPNFRTDSVEGLQEFVKN 184 Query: 189 LFVFYVVFEGMWFYTGFAQILSLGRANKMVGIAEQYQYIMRDESLHLNFGIDVINQIKIE 248 L +Y++ EG++FY+GF ILS R NKM+GI EQYQYI+RDE++HLNFGID+IN IK E Sbjct: 185 LVGYYIIMEGIFFYSGFVMILSFHRQNKMIGIGEQYQYILRDETIHLNFGIDLINGIKEE 244 Query: 249 NPHLWTKEFQQKSRTMLHEATLLEIAYAHETMPKGFVGLNAPSCEQYMQFIANRRCHQIG 308 NP +WT E QQ+ ++ A LEI YA + +P+G +GL A Y+Q IA+RR +IG Sbjct: 245 NPEIWTPELQQEIVELIKRAVDLEIEYAQDCLPRGILGLRASMFIDYVQHIADRRLERIG 304 Query: 309 LEPLFKYTENPFPWMSEVIDLKKEKNFFETRVTEYQQGAELKW 351 L+P++ T+NPFPWMSE IDL KEKNFFETRV EYQ A L W Sbjct: 305 LKPIYH-TKNPFPWMSETIDLNKEKNFFETRVIEYQHAASLTW 346 >1jk0_A RNR Y2, ribonucleoside-diphosphate reductase small chain 1; ribonucleotide reductase, oxidoreductase; 2.80A {Saccharomyces cerevisiae} SCOP: a.25.1.2 PDB: 1smq_A Length = 419 Score = 275 bits (704), Expect = 1e-74 Identities = 95/333 (28%), Positives = 156/333 (46%), Gaps = 27/333 (8%) Query: 21 DKRMLNARSDVNQLLPLKYGWAWEKYLSACNNHWMPTEVPMQDDLALWKSKNGLTDDERL 80 ++ +LN + L P+KY W+ Y A + W E+ + D+ W ++ + ++ER Sbjct: 95 EEPLLNEDKERTVLFPIKYHEIWQAYKRAEASFWTAEEIDLSKDIHDWNNR--MNENERF 152 Query: 81 MIKRNLGFFASSESLVANNIVLAIYRHLSNPECRQYLLRQAFEEAVHSHTFQYIITSLGL 140 I R L FFA+S+ +V N+V + PE + + Q E +HS T+ +I + Sbjct: 153 FISRVLAFFAASDGIVNENLVENFSTEVQIPEAKSFYGFQIMIENIHSETYSLLIDTYIK 212 Query: 141 DEGE---LFNMYREVPSITAKANWALQYTQTLSSPSFTTGTKDADQEFLQDLFVFYVVFE 197 D E LFN +P I KA WAL++ Q + V + E Sbjct: 213 DPKESEFLFNAIHTIPEIGEKAEWALRWIQD-------------ADALFGERLVAFASIE 259 Query: 198 GMWFYTGFAQILSLGRANKMVGIAEQYQYIMRDESLHLNFGIDVINQIKIENPHLWTKEF 257 G++F FA I L + M G+ + I RDE LH +F + +K + ++ Sbjct: 260 GVFFSGSFASIFWLKKRGMMPGLTFSNELICRDEGLHTDFACLLFAHLKNKPDPAIVEK- 318 Query: 258 QQKSRTMLHEATLLEIAYAHETMPKGFVGLNAPSCEQYMQFIANRRCHQIGLEPLFKYTE 317 ++ EA +E Y + +P +G+NA QY++F+A+R G + +K E Sbjct: 319 ------IVTEAVEIEQRYFLDALPVALLGMNADLMNQYVEFVADRLLVAFGNKKYYK-VE 371 Query: 318 NPFPWMSEVIDLKKEKNFFETRVTEYQQGAELK 350 NPF +M E I L + NFFE RV++YQ+ + Sbjct: 372 NPFDFM-ENISLAGKTNFFEKRVSDYQKAGVMS 403 >3dhz_A Ribonucleotide reductase subunit R2F; metal free, hydrogen bond, metal binding protein; 1.63A {Corynebacterium ammoniagenes} SCOP: a.25.1.2 PDB: 1kgo_A 1kgp_A 1oqu_A 1kgn_A 1uzr_A* Length = 329 Score = 272 bits (697), Expect = 8e-74 Identities = 61/322 (18%), Positives = 122/322 (37%), Gaps = 27/322 (8%) Query: 37 LKYGWAWEKYLSACNNHWMPTEVPMQDDLALWKSKNGLTDDERLMIKRNLGFFASSESLV 96 + E + N W+P ++P+ +D+ W +T E+L R +++ Sbjct: 24 IPDEKDLEVWDRLTGNFWLPEKIPVSNDIQSWNK---MTPQEQLATMRVFTGLTLLDTIQ 80 Query: 97 ANNIVLAIYRHLSNPECRQYLLRQAFEEAVHSHTFQYIITSLGLDE--GELFNMYREVPS 154 +++ AF E+VH+ ++ I +L E F E + Sbjct: 81 GTVGAISLLPDAETMHEEAVYTNIAFMESVHAKSYSNIFMTLASTPQINEAFRWSEENEN 140 Query: 155 ITAKANWALQYTQTLSSPSFTTGTKDADQEFLQDLFVFYVVFEGMWFYTGFAQILSLGRA 214 + KA + Y + D + V + E FY+GF + L Sbjct: 141 LQRKAKIIMSYY-------------NGDDPLKK--KVASTLLESFLFYSGFYLPMYLSSR 185 Query: 215 NKMVGIAEQYQYIMRDESLHLNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEATLLEIA 274 K+ A+ + I+RDES+H + Q + +E++ + ++++ EI Sbjct: 186 AKLTNTADIIRLIIRDESVHGYYIGYKYQQGVKKLSEAEQEEYKAYTFDLMYDLYENEIE 245 Query: 275 YAHETMPKGFVGLNAPSCEQYMQFIANRRCHQIGLEPLF---KYTENPFPWMSEVIDLKK 331 Y + +G ++++++ AN+ + +G E LF + +P S + + Sbjct: 246 YTEDIYDD--LGWTE-DVKRFLRYNANKALNNLGYEGLFPTDETKVSPAILSSLSPNADE 302 Query: 332 EKNFFETRVTEYQQG-AELKWD 352 +FF + Y G AE D Sbjct: 303 NHDFFSGSGSSYVIGKAEDTTD 324 >1h0o_A Ribonucleoside-diphosphate reductase; oxidoreductase, ribonucleotide reductase, dinuclear metal-cluster; 2.2A {Mus musculus} SCOP: a.25.1.2 PDB: 1h0n_A 1w68_A 1w69_A 1xsm_A 2uw2_A 3hf1_A 2vux_A Length = 390 Score = 272 bits (696), Expect = 1e-73 Identities = 92/342 (26%), Positives = 155/342 (45%), Gaps = 28/342 (8%) Query: 14 EKRVNVDDKRMLNARSDVNQLLPLKYGWAWEKYLSACNNHWMPTEVPMQDDLALWKSKNG 73 +V+D+ +L + P++Y W+ Y A + W EV + D+ W++ Sbjct: 63 PTNPSVEDEPLLRENPRRFVVFPIEYHDIWQMYKKAEASFWTAEEVDLSKDIQHWEA--- 119 Query: 74 LTDDERLMIKRNLGFFASSESLVANNIVLAIYRHLSNPECRQYLLRQAFEEAVHSHTFQY 133 L DER I L FFA+S+ +V N+V + + E R + Q E +HS + Sbjct: 120 LKPDERHFISHVLAFFAASDGIVNENLVERFSQEVQVTEARCFYGFQIAMENIHSEMYSL 179 Query: 134 IITSLGLDEGELFNM---YREVPSITAKANWALQYTQTLSSPSFTTGTKDADQEFLQDLF 190 +I + D E + +P + KA+WAL++ + + Sbjct: 180 LIDTYIKDPKEREYLFNAIETMPCVKKKADWALRWI-------------GDKEATYGERV 226 Query: 191 VFYVVFEGMWFYTGFAQILSLGRANKMVGIAEQYQYIMRDESLHLNFGIDVINQIKIENP 250 V + EG++F FA I L + M G+ + I RDE LH +F + Sbjct: 227 VAFAAVEGIFFSGSFASIFWLKKRGLMPGLTFSNELISRDEGLHCDFACLMFK------- 279 Query: 251 HLWTKEFQQKSRTMLHEATLLEIAYAHETMPKGFVGLNAPSCEQYMQFIANRRCHQIGLE 310 HL K +Q+ R ++ A +E + E +P +G+N +QY++F+A+R ++G Sbjct: 280 HLVHKPAEQRVREIITNAVRIEQEFLTEALPVKLIGMNCTLMKQYIEFVADRLMLELGFN 339 Query: 311 PLFKYTENPFPWMSEVIDLKKEKNFFETRVTEYQQGAELKWD 352 +F+ ENPF +M I L+ + NFFE RV EYQ+ + Sbjct: 340 KIFR-VENPFDFMEN-ISLEGKTNFFEKRVGEYQRMGVMSNS 379 >1jk0_B RNR Y4, ribonucleoside-diphosphate reductase small chain 2; ribonucleotide reductase, oxidoreductase; 2.80A {Saccharomyces cerevisiae} SCOP: a.25.1.2 PDB: 1sms_A Length = 345 Score = 265 bits (677), Expect = 1e-71 Identities = 72/319 (22%), Positives = 131/319 (41%), Gaps = 27/319 (8%) Query: 34 LLPLKYGWAWEKYLSACNNHWMPTEVPMQDDLALWKSKNGLTDDERLMIKRNLGFFASSE 93 + P+KY W Y + W E+ + D ++ LTDD++ I L SS+ Sbjct: 37 MFPIKYHEIWAAYKKVEASFWTAEEIELAKDTEDFQK---LTDDQKTYIGNLLALSISSD 93 Query: 94 SLVANNIVLAIYRHLSNPECRQYLLRQAFEEAVHSHTFQYIITSLGLDEGE--LFNMYRE 151 +LV ++ L NPE + + Q E ++S + ++ + D LF Sbjct: 94 NLVNKYLIENFSAQLQNPEGKSFYGFQIMMENIYSEVYSMMVDAFFKDPKNIPLFKEIAN 153 Query: 152 VPSITAKANWALQYTQTLSSPSFTTGTKDADQEFLQDLFVFYVVFEGMWFYTGFAQILSL 211 +P + KA + ++ D + V + EG++ +A + L Sbjct: 154 LPEVKHKAAFIERWISN-------------DDSLYAERLVAFAAKEGIFQAGNYASMFWL 200 Query: 212 GRANKMVGIAEQYQYIMRDESLHLNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEATLL 271 M G+A + I RD + +F + HL TK + ++ EA + Sbjct: 201 TDKKIMPGLAMANRNICRDRGAYTDFSCLLFA-------HLRTKPNPKIIEKIITEAVEI 253 Query: 272 EIAYAHETMPKGFVGLNAPSCEQYMQFIANRRCHQIGLEPLFKYTENPFPWMSEVIDLKK 331 E Y ++P G++ S Y++F+A+ G E + NPF +M +V K Sbjct: 254 EKEYYSNSLPVEKFGMDLKSIHTYIEFVADGLLQGFGNEKYYN-AVNPFEFMEDVATAGK 312 Query: 332 EKNFFETRVTEYQQGAELK 350 FFE +V++YQ+ +++ Sbjct: 313 -TTFFEKKVSDYQKASDMS 330 >1mxr_A Ribonucleotide reductase R2; radical protein, DI iron, oxidoreductase; 1.42A {Escherichia coli} SCOP: a.25.1.2 PDB: 1jpr_A 1jqc_A 1xik_A 1yfd_A 1piy_A 1r65_A 1biq_B* 1rsv_A 1piz_A 1piu_A 1pim_A 1rsr_A 1biq_A* 1rib_A 1mrr_A 1rnr_A* 1pj0_A 1pj1_A 1av8_A 1pfr_A ... Length = 375 Score = 259 bits (663), Expect = 6e-70 Identities = 73/340 (21%), Positives = 136/340 (40%), Gaps = 27/340 (7%) Query: 31 VNQLLPLKYGWAWEKYLSACNNHWMPTEVPMQDDLALWKSKNGLTDDERLMIKRNLGFFA 90 V + KY + + W P EV + D +++ L + E+ + NL + Sbjct: 25 VARYDQQKYDIFEKLIEKQLSFFWRPEEVDVSRDRIDYQA---LPEHEKHIFISNLKYQT 81 Query: 91 SSESLVANNIVLAIYRHLSNPECRQYLLRQAFEEAVHSHTFQYIITSLGLDEGELFNMYR 150 +S+ + +A+ +S PE ++ AF E +HS ++ +II ++ D +F+ Sbjct: 82 LLDSIQGRSPNVALLPLISIPELETWVETWAFSETIHSRSYTHIIRNIVNDPSVVFDDIV 141 Query: 151 EVPSITAKANWALQY-----------------TQTLSSPSFTTGTKDADQEFLQDLFVFY 193 I +A Y T T++ + T ++ ++ L + Sbjct: 142 TNEQIQKRAEGISSYYDELIEMTSYWHLLGEGTHTVNGKTVTVSLRELKKKLYLCL-MSV 200 Query: 194 VVFEGMWFYTGFAQILSLGRANKMVGIAEQYQYIMRDESLHLNFGIDVINQIK----IEN 249 E + FY FA + M G A+ + I RDE+LHL ++N ++ Sbjct: 201 NALEAIRFYVSFACSFAFAERELMEGNAKIIRLIARDEALHLTGTQHMLNLLRSGADDPE 260 Query: 250 PHLWTKEFQQKSRTMLHEATLLEIAYAHETM-PKGFVGLNAPSCEQYMQFIANRRCHQIG 308 +E +Q+ + +A E +A +GLN QY+++I N R +G Sbjct: 261 MAEIAEECKQECYDLFVQAAQQEKDWADYLFRDGSMIGLNKDILCQYVEYITNIRMQAVG 320 Query: 309 LEPLFKYTENPFPWMSEVIDLKKEK-NFFETRVTEYQQGA 347 L+ F+ NP PW++ + + E V+ Y G Sbjct: 321 LDLPFQTRSNPIPWINTWLVSDNVQVAPQEVEVSSYLVGQ 360 >3n37_A Ribonucleoside-diphosphate reductase 2 subunit BE; ribonucleotide reductase, four-helix bundle, dimanganese CLU oxidoreductase; 1.65A {Escherichia coli} PDB: 3n38_A 3n39_B* 3n3a_B* 3n3b_B* 1r2f_A 2bq1_I* 2r2f_A Length = 319 Score = 240 bits (614), Expect = 3e-64 Identities = 60/321 (18%), Positives = 119/321 (37%), Gaps = 26/321 (8%) Query: 37 LKYGWAWEKYLSACNNHWMPTEVPMQDDLALWKSKNGLTDDERLMIKRNLGFFASSESLV 96 + E + +N W+P +VP+ +D+ W++ LT E+ + R ++L Sbjct: 14 ISDDKDLEVWNRLTSNFWLPEKVPLSNDIPAWQT---LTVVEQQLTMRVFTGLTLLDTLQ 70 Query: 97 ANNIVLAIYRHLSNPECRQYLLRQAFEEAVHSHTFQYIITSLGL--DEGELFNMYREVPS 154 ++ P L +F EAVH+ ++ I ++L D + E Sbjct: 71 NVIGAPSLMPDALTPHEEAVLSNISFMEAVHARSYSSIFSTLCQTKDVDAAYAWSEENAP 130 Query: 155 ITAKANWALQYTQTLSSPSFTTGTKDADQEFLQDLFVFYVVFEGMWFYTGFAQILSLGRA 214 + KA Q+ + + + V E FY+GF + Sbjct: 131 LQRKAQIIQQHYRG---------------DDPLKKKIASVFLESFLFYSGFWLPMYFSSR 175 Query: 215 NKMVGIAEQYQYIMRDESLHLNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEATLLEIA 274 K+ A+ + I+RDE++H + + + +E + + +L E E+ Sbjct: 176 GKLTNTADLIRLIIRDEAVHGYYIGYKYQKNMEKISLGQREELKSFAFDLLLELYDNELQ 235 Query: 275 YAHETMPKGFVGLNAPSCEQYMQFIANRRCHQIGLEPLF---KYTENPFPWMSEVIDLKK 331 Y E + A + ++ + AN+ +G EPLF NP + + + Sbjct: 236 YTDELYAE---TPWADDVKAFLCYNANKALMNLGYEPLFPAEMAEVNPAILAALSPNADE 292 Query: 332 EKNFFETRVTEYQQGAELKWD 352 +FF + Y G ++ + Sbjct: 293 NHDFFSGSGSSYVMGKAVETE 313 >1r2f_A Protein (ribonucleotide reductase R2); nucleotide metabolism, oxidoreductase; 2.10A {Salmonella typhimurium} SCOP: a.25.1.2 PDB: 2bq1_I* 2r2f_A Length = 319 Score = 239 bits (611), Expect = 6e-64 Identities = 56/321 (17%), Positives = 117/321 (36%), Gaps = 26/321 (8%) Query: 37 LKYGWAWEKYLSACNNHWMPTEVPMQDDLALWKSKNGLTDDERLMIKRNLGFFASSESLV 96 ++ E + +N W+P +VP+ +D+ W++ L+ E+ + R +++ Sbjct: 14 IQDDKDLEVWNRLTSNFWLPEKVPLSNDIPAWQT---LSAAEQQLTIRVFTGLTLLDTIQ 70 Query: 97 ANNIVLAIYRHLSNPECRQYLLRQAFEEAVHSHTFQYIITSLGLDEG--ELFNMYREVPS 154 ++ P L +F EAVH+ ++ I ++L + + E P Sbjct: 71 NIAGAPSLMADAITPHEEAVLSNISFMEAVHARSYSSIFSTLCQTKEVDAAYAWSEENPP 130 Query: 155 ITAKANWALQYTQTLSSPSFTTGTKDADQEFLQDLFVFYVVFEGMWFYTGFAQILSLGRA 214 + KA L + + + V E FY+GF + Sbjct: 131 LQRKAQIILAHY---------------VSDEPLKKKIASVFLESFLFYSGFWLPMYFSSR 175 Query: 215 NKMVGIAEQYQYIMRDESLHLNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEATLLEIA 274 K+ A+ + I+RDE++H + + + +E + + +L E EI Sbjct: 176 GKLTNTADLIRLIIRDEAVHGYYIGYKYQIALQKLSAIEREELKLFALDLLMELYDNEIR 235 Query: 275 YAHETMPKGFVGLNAPSCEQYMQFIANRRCHQIGLEPLF---KYTENPFPWMSEVIDLKK 331 Y + + ++ + AN+ +G E LF NP + + + Sbjct: 236 YTEALYAE---TGWVNDVKAFLCYNANKALMNLGYEALFPPEMADVNPAILAALSPNADE 292 Query: 332 EKNFFETRVTEYQQGAELKWD 352 +FF + Y G ++ + Sbjct: 293 NHDFFSGSGSSYVMGKTVETE 313 >2p1i_A Ribonucleotide reductase, small chain; F222 twinning, plasmodb PY03671, structural genomics consortium, SGC, oxidoreductase; 2.70A {Plasmodium yoelii yoelii str} Length = 349 Score = 222 bits (567), Expect = 7e-59 Identities = 88/338 (26%), Positives = 158/338 (46%), Gaps = 29/338 (8%) Query: 15 KRVNVDDKRMLNARSDVNQLLPLKYGWAWEKYLSACNNHWMPTEVPMQDDLALWKSKNGL 74 ++ ++++LN S+ L P+ Y W Y A + W E+ + DL ++ L Sbjct: 24 QKSKESNEKILNKESNRFTLHPIMYPEVWNFYKKAEASFWTAEEIDLSSDLKDFEK---L 80 Query: 75 TDDERLMIKRNLGFFASSESLVANNIVLAIYRHLSNPECRQYLLRQAFEEAVHSHTFQYI 134 +E+ IK L FFA+S+ +V N+ R + E +++ Q E +HS T+ + Sbjct: 81 NVNEKHFIKHVLAFFAASDGIVLENLASKFLREVEIIEAKKFYSFQIAVENIHSETYSLL 140 Query: 135 ITSLGLD---EGELFNMYREVPSITAKANWALQYTQTLSSPSFTTGTKDADQEFLQDLFV 191 I + D LF+ +P+I KA WA ++ +S + V Sbjct: 141 IDNYIKDEKERLNLFHAIENIPAIKNKALWAAKWINDTNS--------------FAERIV 186 Query: 192 FYVVFEGMWFYTGFAQILSLGRANKMVGIAEQYQYIMRDESLHLNFGIDVINQIKIENPH 251 EG+ F F I + NK+ G+ + I RDE LH +F + + ++ + P Sbjct: 187 ANACVEGILFSGSFCAIFWFKKQNKLHGLTFSNELISRDEGLHTDFNCLIYSLLENKLPE 246 Query: 252 LWTKEFQQKSRTMLHEATLLEIAYAHETMPKGFVGLNAPSCEQYMQFIANRRCHQIGLEP 311 + + EA +E ++ E++P +G+N+ QY++F+A+R +G Sbjct: 247 NVVQNIVK-------EAVEVERSFICESLPCDLIGMNSRLMSQYIEFVADRLLECLGCSK 299 Query: 312 LFKYTENPFPWMSEVIDLKKEKNFFETRVTEYQQGAEL 349 +F ++NPF WM ++I L+ + NFFE RV +YQ+ + Sbjct: 300 VFH-SKNPFNWM-DLISLQGKTNFFEKRVADYQKSGVM 335 >2rcc_A Ribonucleoside-diphosphate reductase subunit beta; NP_241368.1, putative class I ribonucleotide reductase, ribonucleotide reductase; HET: MSE PGE PG4; 1.90A {Bacillus halodurans c-125} Length = 346 Score = 212 bits (540), Expect = 9e-56 Identities = 84/338 (24%), Positives = 159/338 (47%), Gaps = 18/338 (5%) Query: 21 DKRMLNAR-SDVNQLLPLKYGWAWEKYLSACNNHWMPTEVPMQDDLALWKSKNGLTDDER 79 +LN + S+V +++ WA+ Y + N W P E+ M D + + LT+ E+ Sbjct: 19 STGILNGKSSNVLNWDDVRFSWAYPLYKNMLANFWTPFEINMSHDAKQFPT---LTETEQ 75 Query: 80 LMIKRNLGFFASSESLVANNIVLAIYRHLSNPECRQYLLRQAFEEAVHSHTFQYIITSLG 139 K+ +G A +S V + + +L++ + +F+E VH+ ++ Y+++SL Sbjct: 76 EAFKKIIGLLAFLDS-VQTDYSMRAAEYLTDSSLAALMSVLSFQEVVHNQSYSYVLSSLV 134 Query: 140 LDEGE--LFNMYREVPSITAKANWALQYTQTLSSPSFTTGTKDADQEFLQDLFVFYVVFE 197 + +F ++ + + + + + + + + V+ V+ E Sbjct: 135 PKATQDEIFEYWKHDDVLKERNEFIIDGYEKF--------VDNPTPKTFLESIVYDVILE 186 Query: 198 GMWFYTGFAQILSLGRANKMVGIAEQYQYIMRDESLHLNFGIDVINQIKIENPHLWTKEF 257 G+ FY+GFA +L R KMV + YI RDE LH+ ++ ++ +E P L T+E Sbjct: 187 GLNFYSGFAFFYNLARNQKMVSTSTMINYINRDEQLHVYLFTNIFKELLVEFPELNTEET 246 Query: 258 QQKSRTMLHEATLLEIAYAHETMPKGFVGLNAPSCEQYMQFIANRRCHQIGLEPLF-KYT 316 + +T L +A LE + + G+N E Y+ FIAN+R Q+G+E + + Sbjct: 247 KTFVKTTLMKAADLEKDWFRYIIGDKIPGINPEDMETYISFIANKRAVQLGMEKPYPEIK 306 Query: 317 ENPFPWMSEVIDLKKEK-NFFETRVTEYQQG-AELKWD 352 NP W+ D+ K +FFE + +Y + A+ +D Sbjct: 307 HNPMKWIRAYEDVNSGKSDFFEQKSRQYAKVSADNGFD 344 >3mjo_A Ribonucleotide reductase subunit R2F; Mn ribonucleotide reductase, RNR, radical enzyme, split SIGN metallocofactor; 1.36A {Corynebacterium ammoniagenes} PDB: 1uzr_A* Length = 296 Score = 209 bits (532), Expect = 1e-54 Identities = 53/290 (18%), Positives = 109/290 (37%), Gaps = 24/290 (8%) Query: 37 LKYGWAWEKYLSACNNHWMPTEVPMQDDLALWKSKNGLTDDERLMIKRNLGFFASSESLV 96 + E + N W+P ++P+ +D+ W +T E+L R +++ Sbjct: 23 IPDEKDLEVWDRLTGNFWLPEKIPVSNDIQSWNK---MTPQEQLATMRVFTGLTLLDTIQ 79 Query: 97 ANNIVLAIYRHLSNPECRQYLLRQAFEEAVHSHTFQYIITSLGLDEG--ELFNMYREVPS 154 +++ AF E+VH+ ++ I +L E F E + Sbjct: 80 GTVGAISLLPDAETMHEEAVYTNIAFMESVHAKSYSNIFMTLASTPQINEAFRWSEENEN 139 Query: 155 ITAKANWALQYTQTLSSPSFTTGTKDADQEFLQDLFVFYVVFEGMWFYTGFAQILSLGRA 214 + KA + Y + + V + E FY+GF + L Sbjct: 140 LQRKAKIIMSYY---------------NGDDPLKKKVASTLLESFLFYSGFYLPMYLSSR 184 Query: 215 NKMVGIAEQYQYIMRDESLHLNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEATLLEIA 274 K+ A+ + I+RDES+H + Q + +E++ + ++++ EI Sbjct: 185 AKLTNTADIIRLIIRDESVHGYYIGYKYQQGVKKLSEAEQEEYKAYTFDLMYDLYENEIE 244 Query: 275 YAHETMPKGFVGLNAPSCEQYMQFIANRRCHQIGLEPLFKYTENPF-PWM 323 Y + +G ++++++ AN+ + +G E LF E P + Sbjct: 245 YTEDIYDD--LGWTE-DVKRFLRYNANKALNNLGYEGLFPTDETKVSPAI 291 >2o1z_A Ribonucleotide reductase subunit R2; small subunit ribonucleotide reductase, oxidoreductase, DNA replication, iron, DIIRON, radical, R2 subunit; 2.40A {Plasmodium vivax} Length = 311 Score = 202 bits (514), Expect = 1e-52 Identities = 77/306 (25%), Positives = 140/306 (45%), Gaps = 28/306 (9%) Query: 21 DKRMLNARSDVNQLLPLKYGWAWEKYLSACNNHWMPTEVPMQDDLALWKSKNGLTDDERL 80 ++++L+ +D L P+ Y W+ Y A + W E+ + DL ++ L D+E+ Sbjct: 29 NEKILSKETDRFTLYPILYPDVWDFYKKAEASFWTAEEIDLSSDLKDFEK---LNDNEKH 85 Query: 81 MIKRNLGFFASSESLVANNIVLAIYRHLSNPECRQYLLRQAFEEAVHSHTFQYIITSLGL 140 IK L FFA+S+ +V N+ R + E +++ Q E +HS T+ +I + Sbjct: 86 FIKHVLAFFAASDGIVLENLASKFLRQVKITEAKKFYAFQIAVENIHSETYSLLIDNYIK 145 Query: 141 D---EGELFNMYREVPSITAKANWALQYTQTLSSPSFTTGTKDADQEFLQDLFVFYVVFE 197 D LF+ +P++ KA WA ++ D + V E Sbjct: 146 DEKERMNLFHAIENIPAVKNKALWAAKWIN--------------DTNSFAERIVANACVE 191 Query: 198 GMWFYTGFAQILSLGRANKMVGIAEQYQYIMRDESLHLNFGIDVINQIKIENPHLWTKEF 257 G+ F F I + NK+ G+ + I RDE LH +F + + ++ + P + Sbjct: 192 GILFSGSFCAIFWFKKQNKLHGLTFSNELISRDEGLHTDFNCLIYSLLENKLPEEVVQN- 250 Query: 258 QQKSRTMLHEATLLEIAYAHETMPKGFVGLNAPSCEQYMQFIANRRCHQIGLEPLFKYTE 317 ++ EA +E ++ E++P +G+N+ QY++F+A+R +G +F + Sbjct: 251 ------IVKEAVEVERSFICESLPCDLIGMNSRLMSQYIEFVADRLLECLGSPKIFH-AK 303 Query: 318 NPFPWM 323 NPF WM Sbjct: 304 NPFNWM 309 >3ee4_A Probable ribonucleoside-diphosphate reductase; manganese, iron, DIIRON, carboxylate, oxidase, ligand, cavity, monooxygenase; HET: MYR; 1.90A {Mycobacterium tuberculosis} Length = 323 Score = 201 bits (511), Expect = 3e-52 Identities = 51/297 (17%), Positives = 102/297 (34%), Gaps = 20/297 (6%) Query: 46 YLSACNNHWMPTEVPMQDDLALWKSKNGLTDDERLMIKRNLGFFASSESLVANNI--VLA 103 + W P ++ D A W+ L+DDER R F + E V +I ++ Sbjct: 33 FAGGNAKFWHPADIDFTRDRADWEK---LSDDERDYATRLCTQFIAGEEAVTEDIQPFMS 89 Query: 104 IYRHLSNPECRQYLLRQAFEEAVHSHTFQYIITSLGLDEGELFNMYREVPSITAKANWAL 163 R YL + AFEEA H+ F+ + ++G+ E ++P+ L Sbjct: 90 AMRAEGRLADEMYLTQFAFEEAKHTQVFRMWLDAVGISEDL-HRYLDDLPAYRQIFYAEL 148 Query: 164 QYTQTLSSPSFTTGTKDADQEFLQDLFVFYVVFEGMWFYTGFAQILSLG-RANKMVGIAE 222 + ++ + + EGM TG+ + + G+ E Sbjct: 149 PE------CLNALSADPSPAAQVRASVTYNHIVEGMLALTGYYAWHKICVERAILPGMQE 202 Query: 223 QYQYIMRDESLHLNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEATLLEIAYAHETMPK 282 + I DE H+ +G + + W F+ + ++ A L + Sbjct: 203 LVRRIGDDERRHMAWGTFTCRRHVAADDANW-TVFETRMNELIPLALRLIEEGFALYGDQ 261 Query: 283 GFVGLNAPSCEQYMQFIANRRCHQIGLEPLFKYTENPFPWMS-EVIDLKKEKNFFET 338 L+ + ++Q+ ++ + G + P + + + E F + Sbjct: 262 PPFDLSK---DDFLQYSTDKGMRRFGTISNAR--GRPVAEIDVDYSPAQLEDTFADE 313 >2pff_B Fatty acid synthase subunit beta; fatty acid synthase, acyl-carrier-protein, beta-ketoacyl reductase, beta-ketoacyl synthase, dehydratase; 4.00A {Saccharomyces cerevisiae} Length = 2006 Score = 49.9 bits (119), Expect = 9e-07 Identities = 36/284 (12%), Positives = 67/284 (23%), Gaps = 122/284 (42%) Query: 76 DDERLMIKRNLGFFASSESLVANNIVLAIYRHLSNPECRQY--LLR---QAFEEA----- 125 DDE + LV + + + + Q+ +L FE Sbjct: 51 DDE----------PTTPAELVGKFLGY-VSSLVEPSKVGQFDQVLNLCLTEFENCYLEGN 99 Query: 126 -VHSHTFQYIITSLGLDEGELFNMYREVPSITAKANWALQYTQT--LSSPSFTTGTKDAD 182 +H+ + L + ++ Y ++ F + A Sbjct: 100 DIHA-----LAAKLLQEND---------TTLVKTKELIKNYITARIMAKRPFDKKSNSA- 144 Query: 183 QEFLQDLFV--------FYVVFEGM-----WF---------YTGFAQILSLGRANKMVGI 220 LF +F G +F Y L + Sbjct: 145 ------LFRAVGEGNAQLVAIFGGQGNTDDYFEELRDLYQTYHVLVGDL-------IKFS 191 Query: 221 AEQYQYIMRDESL---HLNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEATLLEIAYAH 277 AE ++R G++++ W L Sbjct: 192 AETLSELIRTTLDAEKVFTQGLNILE---------W-----------LENP--------- 222 Query: 278 ETMP-KGFVGLNAP-SCE--------QYMQFIANRRCHQIGLEP 311 P K ++ L+ P SC Y+ + +G P Sbjct: 223 SNTPDKDYL-LSIPISCPLIGVIQLAHYV--VT---AKLLGFTP 260 Score = 36.5 bits (84), Expect = 0.009 Identities = 31/202 (15%), Positives = 52/202 (25%), Gaps = 97/202 (48%) Query: 24 MLNARSDVNQLLPLKYGWAWEKYLSACNNHWMPTEVPMQDDLALWKSKNGLTDDERLMIK 83 ML+ + L + + Y++ N+H L +++ I Sbjct: 338 MLSISN-----LTQE---QVQDYVNKTNSH--------------------LPAGKQVEI- 368 Query: 84 RNLGFFASSESLV--ANNIVLA-----IY---RHLSNPECRQYLLRQA---FEE------ 124 SLV A N+V++ +Y L + L Q+ F E Sbjct: 369 ----------SLVNGAKNLVVSGPPQSLYGLNLTLRKAKAPSG-LDQSRIPFSERKLKFS 417 Query: 125 ------AV--HSH----TFQYIITSLGLDEGEL---------FNMY-----RE-----VP 153 A HSH I L + ++ + R Sbjct: 418 NRFLPVASPFHSHLLVPASDLINKDLVKNNVSFNAKDIQIPVYDTFDGSDLRVLSGSISE 477 Query: 154 S----ITAKA-NW--ALQYTQT 168 I W Q+ T Sbjct: 478 RIVDCIIRLPVKWETTTQFKAT 499 Score = 33.0 bits (75), Expect = 0.11 Identities = 49/222 (22%), Positives = 85/222 (38%), Gaps = 54/222 (24%) Query: 65 LALWKSKNGLTD-----DERLMIKRNLGFFASSESLVANNIV-LAIYRHLSNPECRQYLL 118 + L+K+ D D K GF S +V NN V L I H + ++ + Sbjct: 1633 MDLYKTSKAAQDVWNRADNHF--KDTYGF--SILDIVINNPVNLTI--HFGGEKGKR--I 1684 Query: 119 RQAFEEAVHSHTFQYIITSLGLDEGELFN--MYREV----PSITAKANWAL----QYTQT 168 R+ + + F+ I+ +G+L +++E+ S T ++ L Q+TQ Sbjct: 1685 RENYSAMI----FETIV------DGKLKTEKIFKEINEHSTSYTFRSEKGLLSATQFTQ- 1733 Query: 169 LSSPSFTTGTKDADQEFL-QDLFVFYVVFEG--MWFYTGFAQILSLGRANKMV------G 219 P+ T K A ++ + L F G + Y A + + +V G Sbjct: 1734 ---PALTLMEKAAFEDLKSKGLIPADATFAGHSLGEYAALASLADVMSIESLVEVVFYRG 1790 Query: 220 IAEQYQYIMRDESLHLNFGIDVINQIKIENPHLWTKEFQQKS 261 + Q + RDE N+G+ I NP F Q++ Sbjct: 1791 MTMQVA-VPRDELGRSNYGMIAI------NPGRVAASFSQEA 1825 Score = 29.1 bits (65), Expect = 1.7 Identities = 20/144 (13%), Positives = 44/144 (30%), Gaps = 49/144 (34%) Query: 228 MRDESLH---LNFGIDVINQIKIENP-HLWTKEFQQKSRTMLHEATLLEIAYAHETMPKG 283 R +L L + V P + Q + + L E +G Sbjct: 6 TRPLTLSHGSLEHVLLV--------PTASFFIASQLQEQ---FNKILPEPT-------EG 47 Query: 284 FVGLNAPS-----CEQYMQFIANRRC-HQIG-----LEPLFKYTENPFPWMSEV------ 326 F + P+ +++ ++++ ++G L EN + +++ Sbjct: 48 FAADDEPTTPAELVGKFLGYVSSLVEPSKVGQFDQVLNLCLTEFENCYLEGNDIHALAAK 107 Query: 327 --------IDLKKE--KNFFETRV 340 + KE KN+ R+ Sbjct: 108 LLQENDTTLVKTKELIKNYITARI 131 >3ge3_A Toluene-4-monooxygenase system protein A; DIIRON hydroxylase, effector protein, T201A, aromatic hydrocarbons catabolism, FAD, flavoprotein; 1.52A {Pseudomonas mendocina} PDB: 3ge8_A 3dhi_A* 3dhh_A* 3dhg_A* 3i5j_A 3i63_A Length = 500 Score = 43.7 bits (103), Expect = 7e-05 Identities = 44/221 (19%), Positives = 64/221 (28%), Gaps = 24/221 (10%) Query: 43 WEKYLSACNNHWMPTEVPMQDD---------LALWKSKNGLTDDERLM--IKRNLGFFAS 91 WE Y P V +Q + AL ++K D + +K + G A Sbjct: 44 WESYDEP-YKTSYPEYVSIQREKDAGAYSVKAALERAKIYENSDPGWISTLKSHYGAIAV 102 Query: 92 SESLVANNIVLAIYRHLSNPECRQYLLRQAFEEAVHSHTFQYIITSLGLDEGELFNMYRE 151 E A + R P R +E H + + + +R Sbjct: 103 GE-YAAVTGEGRMARFSKAPGNRNMATFGMMDELRHGQLQLFFPHEYCKKDRQFDWAWRA 161 Query: 152 VPSITAKANWALQYTQTLSSPSFTTGTKDADQEFLQDLFVFYVVFEGMWFYTGFAQILSL 211 WA + T +DA + F F F M + G A + Sbjct: 162 Y----HSNEWAAIAAKHFFDDIITG--RDAISVAIMLTFSFETGFANM-QFLGLAADAA- 213 Query: 212 GRANKMVGIAEQYQYIMRDESLHLNFGIDVINQIKIENPHL 252 A A I DES H G + Q+ IEN Sbjct: 214 -EAGDYT-FANLISSIQTDESRHAQQGGPAL-QLLIENGKR 251 >1mty_D Methane monooxygenase hydroxylase; dinuclear iron center monooxygenase; 1.70A {Methylococcus capsulatus str} SCOP: a.25.1.2 PDB: 1mmo_D 1xvb_A 1fyz_A 1fz0_A 1fz2_A 1fz3_A 1fz4_A 1fz5_A 1fz6_A 1fz7_A 1fz8_A 1fz9_A 1fzh_A 1fzi_A 1xmf_A 1xmg_A 1xmh_A 1xu3_A 1xu5_A 1fz1_A ... Length = 512 Score = 33.3 bits (76), Expect = 0.082 Identities = 24/146 (16%), Positives = 39/146 (26%), Gaps = 8/146 (5%) Query: 106 RHLSNPECRQYLLRQAFEEAVHSHTFQYIITSLGLDEGELFNMYREVPSITAKANWALQY 165 E + L Q +E H+H Y+ + + T + Sbjct: 112 DSAQAAEQKNGYLAQVLDEIRHTHQCAYVNYYFAKNGQDPAGHNDA--RRTRTIGPLWKG 169 Query: 166 TQTLSSPSFTTGTKDADQEFLQDLFVFYVVFEGMWFYTGFAQILSLGRANKMVGIAEQYQ 225 + + S F +G DA + L V F AN + Sbjct: 170 MKRVFSDGFISG--DAVECSLNLQLVGEACFTNP-LIVAVT---EWAAANGDEITPTVFL 223 Query: 226 YIMRDESLHLNFGIDVINQIKIENPH 251 I DE H+ G + I + Sbjct: 224 SIETDELRHMANGYQTVVSIANDPAS 249 >2pff_A Fatty acid synthase subunit alpha, 3-oxoacyl-[acyl-carrier-; fatty acid synthase, acyl-carrier-protein, beta-ketoacyl reductase, beta-ketoacyl synthase, dehydratase; 4.00A {Saccharomyces cerevisiae} Length = 1688 Score = 30.2 bits (67), Expect = 0.72 Identities = 12/37 (32%), Positives = 19/37 (51%), Gaps = 6/37 (16%) Query: 198 GMWFYTGFAQILSLG------RANKMVGIAEQYQYIM 228 G W G QIL+ G A+ + I EQ++Y++ Sbjct: 1390 GAWMMNGALQILNSGIIPGNRNADNVDKILEQFEYVL 1426 Score = 27.9 bits (61), Expect = 4.1 Identities = 27/96 (28%), Positives = 34/96 (35%), Gaps = 34/96 (35%) Query: 223 QYQYIMRDESLHLNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEA----------TLLE 272 Q +M D LN G+ + P L KEF K R L E T LE Sbjct: 719 QKSPVMAD----LNGGLQFV-------PEL--KEFTAKLRKELVETSEVRKAVSIETALE 765 Query: 273 ----------IAYAH-ETMPKGFVGLNAPSCEQYMQ 297 AYA E P+ + L+ P + Y Q Sbjct: 766 HKVVNGNSADAAYAQVEIQPRANIQLDFPELKPYKQ 801 >3chh_A P-aminobenzoate N-oxygenase; DI-iron oxygenase, oxidoreductase; 2.00A {Streptomyces thioluteus} PDB: 3chi_A 3cht_A* 3chu_A 2jcd_A Length = 336 Score = 28.0 bits (62), Expect = 3.4 Identities = 7/44 (15%), Positives = 20/44 (45%), Gaps = 4/44 (9%) Query: 93 ESLVAN----NIVLAIYRHLSNPECRQYLLRQAFEEAVHSHTFQ 132 E L+A ++ ++ +P R+ + + +E+ H++ Sbjct: 101 EQLIAEPAFDLVMHGVFPGSDDPLIRKSVQQAIVDESFHTYMHM 144 >3dsk_A Cytochrome P450 74A, chloroplast; P450 fold, fatty acid biosynthesis, heme, iron, lipid synthesis, lyase, metal-binding; HET: HEM T25; 1.55A {Arabidopsis thaliana} PDB: 2rcm_A* 3dsj_A* 3dsi_A* 2rcl_A* 2rch_A* 3cli_A* Length = 495 Score = 27.9 bits (61), Expect = 3.5 Identities = 7/68 (10%), Positives = 20/68 (29%), Gaps = 3/68 (4%) Query: 63 DDLALWKSKNGLTDDERLMIKRNLGFFASSESLVANNIVLAIYRHLS-NPECRQYLLRQA 121 ++ + K G++ +E F + + + R + L + Sbjct: 267 GEILVEADKLGISREEATHNLLFATCFNTWGG-MKILFPNMVKRIGRAGHQV-HNRLAEE 324 Query: 122 FEEAVHSH 129 + S+ Sbjct: 325 IRSVIKSN 332 >1znw_A Guanylate kinase, GMP kinase; ATP:GMP-phosphotransferase; 2.10A {Mycobacterium tuberculosis} SCOP: c.37.1.1 PDB: 1znx_A* 1zny_A* 1znz_A* 1s4q_A 1z8f_A Length = 207 Score = 27.3 bits (59), Expect = 4.9 Identities = 7/37 (18%), Positives = 12/37 (32%) Query: 106 RHLSNPECRQYLLRQAFEEAVHSHTFQYIITSLGLDE 142 R + Q L A E F ++ + L+ Sbjct: 154 RGTETADVIQRRLDTARIELAAQGDFDKVVVNRRLES 190 >2e0z_A Virus-like particle; bacteriophage, HK97; 3.60A {Pyrococcus furiosus} Length = 345 Score = 27.1 bits (60), Expect = 6.2 Identities = 22/88 (25%), Positives = 37/88 (42%), Gaps = 5/88 (5%) Query: 74 LTDDERLMIKRNLGFFASSESLVANNIVLAIYRHLSNPECRQYLLRQAFEEAVHSHTFQY 133 T +E + L +E L A N+ + R+ + R+ LL A EE H F Sbjct: 15 YTKEE---LMEILRLAIIAE-LDAINLYEQMARYSEDENVRKILLDVAREEKAHVGEFMA 70 Query: 134 IITSLGLDE-GELFNMYREVPSITAKAN 160 ++ +L ++ EL + EV +T Sbjct: 71 LLLNLDPEQVTELKGGFEEVKELTGIEA 98 >3dan_A Cytochrome P450 74A2; AOS heme cytochrome P450 structure, fatty acid biosynthesis, heme, iron, lipid synthesis, lyase, metal-binding; HET: HEM; 1.80A {Parthenium argentatum} PDB: 3dam_A* 3dbm_A* Length = 473 Score = 26.8 bits (58), Expect = 8.3 Identities = 10/72 (13%), Positives = 19/72 (26%), Gaps = 1/72 (1%) Query: 63 DDLALWKSKNGLTDDERLMIKRNLGFFASSESLVANNIVLAIYRHLSNPECRQYLLRQAF 122 + K G+ DE + F + V + E L + Sbjct: 249 TPVMEQAEKLGVPKDEAVHNILFAVCFNTFGG-VKILFPNTLKWIGLAGENLHTQLAEEI 307 Query: 123 EEAVHSHTFQYI 134 A+ S+ + Sbjct: 308 RGAIKSYGDGNV 319 Database: pdb70 Posted date: Jan 26, 2011 11:21 AM Number of letters in database: 5,693,230 Number of sequences in database: 24,244 Lambda K H 0.320 0.134 0.412 Gapped Lambda K H 0.267 0.0499 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 24244 Number of Hits to DB: 3,041,079 Number of extensions: 136783 Number of successful extensions: 380 Number of sequences better than 10.0: 1 Number of HSP's gapped: 318 Number of HSP's successfully gapped: 31 Length of query: 352 Length of database: 5,693,230 Length adjustment: 93 Effective length of query: 259 Effective length of database: 3,438,538 Effective search space: 890581342 Effective search space used: 890581342 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: 57 (26.3 bits)