RPS-BLAST 2.2.22 [Sep-27-2009] Database: pdb70 24,244 sequences; 5,693,230 total letters Searching..................................................done Query= 537021.9.peg.75_1 (136 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 = 137 bits (347), Expect = 5e-34 Identities = 80/135 (59%), Positives = 100/135 (74%), Gaps = 1/135 (0%) Query: 1 MVGIAEQYQYIMRDESLHLNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEATLLEIAYA 60 M+GI EQYQYI+RDE++HLNFGID+IN IK ENP +WT E QQ+ ++ A LEI YA Sbjct: 213 MIGIGEQYQYILRDETIHLNFGIDLINGIKEENPEIWTPELQQEIVELIKRAVDLEIEYA 272 Query: 61 HETMPKGFVGLNAPSCEQYMQFIANRRCHQIGLEPLFKYTENPFPWMSEVIDLKKEKNFF 120 + +P+G +GL A Y+Q IA+RR +IGL+P++ T+NPFPWMSE IDL KEKNFF Sbjct: 273 QDCLPRGILGLRASMFIDYVQHIADRRLERIGLKPIYH-TKNPFPWMSETIDLNKEKNFF 331 Query: 121 ETRVTEYQQGAGLKW 135 ETRV EYQ A L W Sbjct: 332 ETRVIEYQHAASLTW 346 >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 = 123 bits (310), Expect = 1e-29 Identities = 25/134 (18%), Positives = 57/134 (42%), Gaps = 6/134 (4%) Query: 1 MVGIAEQYQYIMRDESLHLNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEATLLEIAYA 60 + A+ + I+RDES+H + Q + +E++ + ++++ EI Y Sbjct: 188 LTNTADIIRLIIRDESVHGYYIGYKYQQGVKKLSEAEQEEYKAYTFDLMYDLYENEIEYT 247 Query: 61 HETMPKGFVGLNAPSCEQYMQFIANRRCHQIGLEPLF---KYTENPFPWMSEVIDLKKEK 117 + +G ++++++ AN+ + +G E LF + +P S + + Sbjct: 248 EDIYDD--LGWTE-DVKRFLRYNANKALNNLGYEGLFPTDETKVSPAILSSLSPNADENH 304 Query: 118 NFFETRVTEYQQGA 131 +FF + Y G Sbjct: 305 DFFSGSGSSYVIGK 318 >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 = 123 bits (310), Expect = 1e-29 Identities = 43/136 (31%), Positives = 70/136 (51%), Gaps = 9/136 (6%) Query: 1 MVGIAEQYQYIMRDESLHLNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEATLLEIAYA 60 M G+ + I RDE LH +F + HL K +Q+ R ++ A +E + Sbjct: 253 MPGLTFSNELISRDEGLHCDFACLMFK-------HLVHKPAEQRVREIITNAVRIEQEFL 305 Query: 61 HETMPKGFVGLNAPSCEQYMQFIANRRCHQIGLEPLFKYTENPFPWMSEVIDLKKEKNFF 120 E +P +G+N +QY++F+A+R ++G +F+ ENPF +M I L+ + NFF Sbjct: 306 TEALPVKLIGMNCTLMKQYIEFVADRLMLELGFNKIFR-VENPFDFMEN-ISLEGKTNFF 363 Query: 121 ETRVTEYQQGAGLKWD 136 E RV EYQ+ + Sbjct: 364 EKRVGEYQRMGVMSNS 379 >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 = 119 bits (298), Expect = 3e-28 Identities = 41/131 (31%), Positives = 67/131 (51%), Gaps = 9/131 (6%) Query: 1 MVGIAEQYQYIMRDESLHLNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEATLLEIAYA 60 M G+ + I RDE LH +F + +K + ++ ++ EA +E Y Sbjct: 279 MPGLTFSNELICRDEGLHTDFACLLFAHLKNKPDPAIVEK-------IVTEAVEIEQRYF 331 Query: 61 HETMPKGFVGLNAPSCEQYMQFIANRRCHQIGLEPLFKYTENPFPWMSEVIDLKKEKNFF 120 + +P +G+NA QY++F+A+R G + +K ENPF +M E I L + NFF Sbjct: 332 LDALPVALLGMNADLMNQYVEFVADRLLVAFGNKKYYK-VENPFDFM-ENISLAGKTNFF 389 Query: 121 ETRVTEYQQGA 131 E RV++YQ+ Sbjct: 390 EKRVSDYQKAG 400 >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 = 119 bits (298), Expect = 3e-28 Identities = 35/137 (25%), Positives = 60/137 (43%), Gaps = 6/137 (4%) Query: 1 MVGIAEQYQYIMRDESLHLNFGIDVINQIK----IENPHLWTKEFQQKSRTMLHEATLLE 56 M G A+ + I RDE+LHL ++N ++ +E +Q+ + +A E Sbjct: 224 MEGNAKIIRLIARDEALHLTGTQHMLNLLRSGADDPEMAEIAEECKQECYDLFVQAAQQE 283 Query: 57 IAYAHETM-PKGFVGLNAPSCEQYMQFIANRRCHQIGLEPLFKYTENPFPWMSEVIDLKK 115 +A +GLN QY+++I N R +GL+ F+ NP PW++ + Sbjct: 284 KDWADYLFRDGSMIGLNKDILCQYVEYITNIRMQAVGLDLPFQTRSNPIPWINTWLVSDN 343 Query: 116 EK-NFFETRVTEYQQGA 131 + E V+ Y G Sbjct: 344 VQVAPQEVEVSSYLVGQ 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 = 118 bits (296), Expect = 5e-28 Identities = 26/139 (18%), Positives = 55/139 (39%), Gaps = 6/139 (4%) Query: 1 MVGIAEQYQYIMRDESLHLNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEATLLEIAYA 60 + A+ + I+RDE++H + + + +E + + +L E E+ Y Sbjct: 178 LTNTADLIRLIIRDEAVHGYYIGYKYQKNMEKISLGQREELKSFAFDLLLELYDNELQYT 237 Query: 61 HETMPKGFVGLNAPSCEQYMQFIANRRCHQIGLEPLF---KYTENPFPWMSEVIDLKKEK 117 E + A + ++ + AN+ +G EPLF NP + + + Sbjct: 238 DELYAET---PWADDVKAFLCYNANKALMNLGYEPLFPAEMAEVNPAILAALSPNADENH 294 Query: 118 NFFETRVTEYQQGAGLKWD 136 +FF + Y G ++ + Sbjct: 295 DFFSGSGSSYVMGKAVETE 313 >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 = 112 bits (282), Expect = 2e-26 Identities = 35/134 (26%), Positives = 61/134 (45%), Gaps = 9/134 (6%) Query: 1 MVGIAEQYQYIMRDESLHLNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEATLLEIAYA 60 M G+A + I RD + +F + HL TK + ++ EA +E Y Sbjct: 206 MPGLAMANRNICRDRGAYTDFSCLLFA-------HLRTKPNPKIIEKIITEAVEIEKEYY 258 Query: 61 HETMPKGFVGLNAPSCEQYMQFIANRRCHQIGLEPLFKYTENPFPWMSEVIDLKKEKNFF 120 ++P G++ S Y++F+A+ G E + NPF +M +V K FF Sbjct: 259 SNSLPVEKFGMDLKSIHTYIEFVADGLLQGFGNEKYYN-AVNPFEFMEDVATAGK-TTFF 316 Query: 121 ETRVTEYQQGAGLK 134 E +V++YQ+ + + Sbjct: 317 EKKVSDYQKASDMS 330 >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 = 112 bits (281), Expect = 3e-26 Identities = 24/139 (17%), Positives = 52/139 (37%), Gaps = 6/139 (4%) Query: 1 MVGIAEQYQYIMRDESLHLNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEATLLEIAYA 60 + A+ + I+RDE++H + + + +E + + +L E EI Y Sbjct: 178 LTNTADLIRLIIRDEAVHGYYIGYKYQIALQKLSAIEREELKLFALDLLMELYDNEIRYT 237 Query: 61 HETMPKGFVGLNAPSCEQYMQFIANRRCHQIGLEPLF---KYTENPFPWMSEVIDLKKEK 117 + + ++ + AN+ +G E LF NP + + + Sbjct: 238 EALYAET---GWVNDVKAFLCYNANKALMNLGYEALFPPEMADVNPAILAALSPNADENH 294 Query: 118 NFFETRVTEYQQGAGLKWD 136 +FF + Y G ++ + Sbjct: 295 DFFSGSGSSYVMGKTVETE 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 = 101 bits (253), Expect = 4e-23 Identities = 38/131 (29%), Positives = 71/131 (54%), Gaps = 9/131 (6%) Query: 1 MVGIAEQYQYIMRDESLHLNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEATLLEIAYA 60 + G+ + I RDE LH +F + + ++ + P + + EA +E ++ Sbjct: 212 LHGLTFSNELISRDEGLHTDFNCLIYSLLENKLPENVVQNIVK-------EAVEVERSFI 264 Query: 61 HETMPKGFVGLNAPSCEQYMQFIANRRCHQIGLEPLFKYTENPFPWMSEVIDLKKEKNFF 120 E++P +G+N+ QY++F+A+R +G +F ++NPF WM ++I L+ + NFF Sbjct: 265 CESLPCDLIGMNSRLMSQYIEFVADRLLECLGCSKVFH-SKNPFNWM-DLISLQGKTNFF 322 Query: 121 ETRVTEYQQGA 131 E RV +YQ+ Sbjct: 323 EKRVADYQKSG 333 >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 = 96.4 bits (239), Expect = 2e-21 Identities = 40/133 (30%), Positives = 67/133 (50%), Gaps = 2/133 (1%) Query: 1 MVGIAEQYQYIMRDESLHLNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEATLLEIAYA 60 MV + YI RDE LH+ ++ ++ +E P L T+E + +T L +A LE + Sbjct: 206 MVSTSTMINYINRDEQLHVYLFTNIFKELLVEFPELNTEETKTFVKTTLMKAADLEKDWF 265 Query: 61 HETMPKGFVGLNAPSCEQYMQFIANRRCHQIGLEPLF-KYTENPFPWMSEVIDLKKEK-N 118 + G+N E Y+ FIAN+R Q+G+E + + NP W+ D+ K + Sbjct: 266 RYIIGDKIPGINPEDMETYISFIANKRAVQLGMEKPYPEIKHNPMKWIRAYEDVNSGKSD 325 Query: 119 FFETRVTEYQQGA 131 FFE + +Y + + Sbjct: 326 FFEQKSRQYAKVS 338 >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 = 87.4 bits (216), Expect = 9e-19 Identities = 21/108 (19%), Positives = 48/108 (44%), Gaps = 4/108 (3%) Query: 1 MVGIAEQYQYIMRDESLHLNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEATLLEIAYA 60 + A+ + I+RDES+H + Q + +E++ + ++++ EI Y Sbjct: 187 LTNTADIIRLIIRDESVHGYYIGYKYQQGVKKLSEAEQEEYKAYTFDLMYDLYENEIEYT 246 Query: 61 HETMPKGFVGLNAPSCEQYMQFIANRRCHQIGLEPLFKYTENPF-PWM 107 + +G ++++++ AN+ + +G E LF E P + Sbjct: 247 EDIYDD--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 = 85.6 bits (211), Expect = 3e-18 Identities = 28/107 (26%), Positives = 55/107 (51%), Gaps = 8/107 (7%) Query: 1 MVGIAEQYQYIMRDESLHLNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEATLLEIAYA 60 + G+ + I RDE LH +F + + ++ + P + ++ EA +E ++ Sbjct: 211 LHGLTFSNELISRDEGLHTDFNCLIYSLLENKLPEEVVQN-------IVKEAVEVERSFI 263 Query: 61 HETMPKGFVGLNAPSCEQYMQFIANRRCHQIGLEPLFKYTENPFPWM 107 E++P +G+N+ QY++F+A+R +G +F +NPF WM Sbjct: 264 CESLPCDLIGMNSRLMSQYIEFVADRLLECLGSPKIFH-AKNPFNWM 309 >3ee4_A Probable ribonucleoside-diphosphate reductase; manganese, iron, DIIRON, carboxylate, oxidase, ligand, cavity, monooxygenase; HET: MYR; 1.90A {Mycobacterium tuberculosis} Length = 323 Score = 84.8 bits (209), Expect = 6e-18 Identities = 17/123 (13%), Positives = 42/123 (34%), Gaps = 7/123 (5%) Query: 1 MVGIAEQYQYIMRDESLHLNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEATLLEIAYA 60 + G+ E + I DE H+ +G + + W F+ + ++ A L Sbjct: 197 LPGMQELVRRIGDDERRHMAWGTFTCRRHVAADDANW-TVFETRMNELIPLALRLIEEGF 255 Query: 61 HETMPKGFVGLNAPSCEQYMQFIANRRCHQIGLEPLFKYTENPFPWMS-EVIDLKKEKNF 119 + L+ + ++Q+ ++ + G + P + + + E F Sbjct: 256 ALYGDQPPFDLSK---DDFLQYSTDKGMRRFGTISNAR--GRPVAEIDVDYSPAQLEDTF 310 Query: 120 FET 122 + Sbjct: 311 ADE 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 = 29.5 bits (66), Expect = 0.26 Identities = 15/105 (14%), Positives = 27/105 (25%), Gaps = 48/105 (45%) Query: 4 IAEQYQYIMRDESL---HLNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEATLLEIAYA 60 AE ++R G++++ W L Sbjct: 191 SAETLSELIRTTLDAEKVFTQGLNILE---------W-----------LENP-------- 222 Query: 61 HETMP-KGFVGLNAP-SCE--------QYMQFIANRRCHQIGLEP 95 P K ++ L+ P SC Y+ + +G P Sbjct: 223 -SNTPDKDYL-LSIPISCPLIGVIQLAHYV--VT---AKLLGFTP 260 Score = 29.1 bits (65), Expect = 0.37 Identities = 20/144 (13%), Positives = 44/144 (30%), Gaps = 49/144 (34%) Query: 12 MRDESLH---LNFGIDVINQIKIENP-HLWTKEFQQKSRTMLHEATLLEIAYAHETMPKG 67 R +L L + V P + Q + + L E +G Sbjct: 6 TRPLTLSHGSLEHVLLV--------PTASFFIASQLQEQ---FNKILPEPT-------EG 47 Query: 68 FVGLNAPS-----CEQYMQFIANRRC-HQIG-----LEPLFKYTENPFPWMSEV------ 110 F + P+ +++ ++++ ++G L EN + +++ Sbjct: 48 FAADDEPTTPAELVGKFLGYVSSLVEPSKVGQFDQVLNLCLTEFENCYLEGNDIHALAAK 107 Query: 111 --------IDLKKE--KNFFETRV 124 + KE KN+ R+ Sbjct: 108 LLQENDTTLVKTKELIKNYITARI 131 >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 = 27.1 bits (59), Expect = 1.3 Identities = 27/96 (28%), Positives = 34/96 (35%), Gaps = 34/96 (35%) Query: 7 QYQYIMRDESLHLNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEA----------TLLE 56 Q +M D LN G+ + P L KEF K R L E T LE Sbjct: 719 QKSPVMAD----LNGGLQFV-------PEL--KEFTAKLRKELVETSEVRKAVSIETALE 765 Query: 57 ----------IAYAH-ETMPKGFVGLNAPSCEQYMQ 81 AYA E P+ + L+ P + Y Q Sbjct: 766 HKVVNGNSADAAYAQVEIQPRANIQLDFPELKPYKQ 801 >1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant photosynthetic reaction center, peripheral antenna; HET: CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1 Length = 154 Score = 26.1 bits (56), Expect = 3.0 Identities = 7/25 (28%), Positives = 14/25 (56%), Gaps = 6/25 (24%) Query: 42 QQKSRTMLHEATL-LEIAYAHETMP 65 +Q + + +A+L L YA ++ P Sbjct: 19 KQALKKL--QASLKL---YADDSAP 38 >2x5y_A Zinc finger CCCH-type antiviral protein 1; antiviral defense, immune system, transferase; 1.05A {Homo sapiens} Length = 173 Score = 24.9 bits (54), Expect = 6.0 Identities = 12/34 (35%), Positives = 13/34 (38%), Gaps = 1/34 (2%) Query: 22 GIDVINQIKIENPHLWTKEFQQKSRTMLHEATLL 55 + KIEN L K F K M E LL Sbjct: 30 NFKIEKIKKIENSELLDK-FTWKKSQMKEEGKLL 62 >2oc5_A Hypothetical protein; NP_895059.1, structural genomics, joint center for structural genomics, JCSG, protein structure initiative; HET: UNL; 1.68A {Prochlorococcus marinus str} SCOP: a.25.1.6 Length = 244 Score = 24.8 bits (54), Expect = 6.0 Identities = 6/12 (50%), Positives = 10/12 (83%) Query: 11 IMRDESLHLNFG 22 +++DE HLN+G Sbjct: 154 VVKDEYTHLNYG 165 >3e49_A Uncharacterized protein DUF849 with A TIM barrel fold; YP_556190.1; HET: MSE; 1.75A {Burkholderia xenovorans LB400} Length = 311 Score = 24.6 bits (53), Expect = 7.4 Identities = 12/48 (25%), Positives = 25/48 (52%) Query: 19 LNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEATLLEIAYAHETMPK 66 +NFG+ + + E H W +E ++SR ++ + T +I + +T Sbjct: 117 MNFGLYPMLERFKEFAHGWEREHLERSRDLVFKNTFADIEFILKTCGG 164 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 0.321 0.136 0.422 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: 1,191,654 Number of extensions: 49721 Number of successful extensions: 152 Number of sequences better than 10.0: 1 Number of HSP's gapped: 126 Number of HSP's successfully gapped: 31 Length of query: 136 Length of database: 5,693,230 Length adjustment: 83 Effective length of query: 53 Effective length of database: 3,680,978 Effective search space: 195091834 Effective search space used: 195091834 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 (21.9 bits) S2: 51 (24.0 bits)