RPS-BLAST 2.2.22 [Sep-27-2009] Database: pdb70 24,244 sequences; 5,693,230 total letters Searching..................................................done Query= gi|254781006|ref|YP_003065419.1| ribonucleotide-diphosphate reductase subunit beta [Candidatus Liberibacter asiaticus str. psy62] (125 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 = 127 bits (319), Expect = 9e-31 Identities = 71/124 (57%), Positives = 90/124 (72%), Gaps = 1/124 (0%) Query: 1 MRDESLHLNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEATLLEIAYAHETMPKGFVGL 60 +RDE++HLNFGID+IN IK ENP +WT E QQ+ ++ A LEI YA + +P+G +GL Sbjct: 224 LRDETIHLNFGIDLINGIKEENPEIWTPELQQEIVELIKRAVDLEIEYAQDCLPRGILGL 283 Query: 61 NAPSCEQYMQFIANRRCHQIGLEPLFKYTENPFPWMSEVIDLKKEKNFFETRVTEYQQGA 120 A Y+Q IA+RR +IGL+P++ T+NPFPWMSE IDL KEKNFFETRV EYQ A Sbjct: 284 RASMFIDYVQHIADRRLERIGLKPIYH-TKNPFPWMSETIDLNKEKNFFETRVIEYQHAA 342 Query: 121 ELKW 124 L W Sbjct: 343 SLTW 346 >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 = 112 bits (280), Expect = 3e-26 Identities = 40/125 (32%), Positives = 65/125 (52%), Gaps = 9/125 (7%) Query: 1 MRDESLHLNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEATLLEIAYAHETMPKGFVGL 60 RDE LH +F + HL K +Q+ R ++ A +E + E +P +G+ Sbjct: 264 SRDEGLHCDFACLMFK-------HLVHKPAEQRVREIITNAVRIEQEFLTEALPVKLIGM 316 Query: 61 NAPSCEQYMQFIANRRCHQIGLEPLFKYTENPFPWMSEVIDLKKEKNFFETRVTEYQQGA 120 N +QY++F+A+R ++G +F+ ENPF +M I L+ + NFFE RV EYQ+ Sbjct: 317 NCTLMKQYIEFVADRLMLELGFNKIFR-VENPFDFMEN-ISLEGKTNFFEKRVGEYQRMG 374 Query: 121 ELKWD 125 + Sbjct: 375 VMSNS 379 >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 = 111 bits (279), Expect = 4e-26 Identities = 26/129 (20%), Positives = 55/129 (42%), Gaps = 7/129 (5%) Query: 1 MRDESLHLNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEATLLEIAYAHETMPKGFVGL 60 +RDES+H + Q + +E++ + ++++ EI Y + +G Sbjct: 199 IRDESVHGYYIGYKYQQGVKKLSEAEQEEYKAYTFDLMYDLYENEIEYTEDIYDD--LGW 256 Query: 61 NAPSCEQYMQFIANRRCHQIGLEPLF---KYTENPFPWMSEVIDLKKEKNFFETRVTEYQ 117 ++++++ AN+ + +G E LF + +P S + + +FF + Y Sbjct: 257 TE-DVKRFLRYNANKALNNLGYEGLFPTDETKVSPAILSSLSPNADENHDFFSGSGSSYV 315 Query: 118 QG-AELKWD 125 G AE D Sbjct: 316 IGKAEDTTD 324 >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 = 108 bits (270), Expect = 4e-25 Identities = 38/123 (30%), Positives = 63/123 (51%), Gaps = 9/123 (7%) Query: 1 MRDESLHLNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEATLLEIAYAHETMPKGFVGL 60 RDE LH +F + +K + ++ ++ EA +E Y + +P +G+ Sbjct: 290 CRDEGLHTDFACLLFAHLKNKPDPAIVEK-------IVTEAVEIEQRYFLDALPVALLGM 342 Query: 61 NAPSCEQYMQFIANRRCHQIGLEPLFKYTENPFPWMSEVIDLKKEKNFFETRVTEYQQGA 120 NA QY++F+A+R G + +K ENPF +M E I L + NFFE RV++YQ+ Sbjct: 343 NADLMNQYVEFVADRLLVAFGNKKYYK-VENPFDFM-ENISLAGKTNFFEKRVSDYQKAG 400 Query: 121 ELK 123 + Sbjct: 401 VMS 403 >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 = 106 bits (265), Expect = 2e-24 Identities = 31/126 (24%), Positives = 54/126 (42%), Gaps = 6/126 (4%) Query: 1 MRDESLHLNFGIDVINQIK----IENPHLWTKEFQQKSRTMLHEATLLEIAYAHETM-PK 55 RDE+LHL ++N ++ +E +Q+ + +A E +A Sbjct: 235 ARDEALHLTGTQHMLNLLRSGADDPEMAEIAEECKQECYDLFVQAAQQEKDWADYLFRDG 294 Query: 56 GFVGLNAPSCEQYMQFIANRRCHQIGLEPLFKYTENPFPWMSEVIDLKKEK-NFFETRVT 114 +GLN QY+++I N R +GL+ F+ NP PW++ + + E V+ Sbjct: 295 SMIGLNKDILCQYVEYITNIRMQAVGLDLPFQTRSNPIPWINTWLVSDNVQVAPQEVEVS 354 Query: 115 EYQQGA 120 Y G Sbjct: 355 SYLVGQ 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 = 106 bits (264), Expect = 2e-24 Identities = 24/128 (18%), Positives = 50/128 (39%), Gaps = 6/128 (4%) Query: 1 MRDESLHLNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEATLLEIAYAHETMPKGFVGL 60 +RDE++H + + + +E + + +L E E+ Y E + Sbjct: 189 IRDEAVHGYYIGYKYQKNMEKISLGQREELKSFAFDLLLELYDNELQYTDELYAET---P 245 Query: 61 NAPSCEQYMQFIANRRCHQIGLEPLF---KYTENPFPWMSEVIDLKKEKNFFETRVTEYQ 117 A + ++ + AN+ +G EPLF NP + + + +FF + Y Sbjct: 246 WADDVKAFLCYNANKALMNLGYEPLFPAEMAEVNPAILAALSPNADENHDFFSGSGSSYV 305 Query: 118 QGAELKWD 125 G ++ + Sbjct: 306 MGKAVETE 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 = 103 bits (257), Expect = 1e-23 Identities = 31/123 (25%), Positives = 56/123 (45%), Gaps = 9/123 (7%) Query: 1 MRDESLHLNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEATLLEIAYAHETMPKGFVGL 60 RD + +F + HL TK + ++ EA +E Y ++P G+ Sbjct: 217 CRDRGAYTDFSCLLFA-------HLRTKPNPKIIEKIITEAVEIEKEYYSNSLPVEKFGM 269 Query: 61 NAPSCEQYMQFIANRRCHQIGLEPLFKYTENPFPWMSEVIDLKKEKNFFETRVTEYQQGA 120 + S Y++F+A+ G E + NPF +M +V K FFE +V++YQ+ + Sbjct: 270 DLKSIHTYIEFVADGLLQGFGNEKYYN-AVNPFEFMEDVATAGK-TTFFEKKVSDYQKAS 327 Query: 121 ELK 123 ++ Sbjct: 328 DMS 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 = 100 bits (251), Expect = 6e-23 Identities = 22/128 (17%), Positives = 47/128 (36%), Gaps = 6/128 (4%) Query: 1 MRDESLHLNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEATLLEIAYAHETMPKGFVGL 60 +RDE++H + + + +E + + +L E EI Y + Sbjct: 189 IRDEAVHGYYIGYKYQIALQKLSAIEREELKLFALDLLMELYDNEIRYTEALYAET---G 245 Query: 61 NAPSCEQYMQFIANRRCHQIGLEPLF---KYTENPFPWMSEVIDLKKEKNFFETRVTEYQ 117 + ++ + AN+ +G E LF NP + + + +FF + Y Sbjct: 246 WVNDVKAFLCYNANKALMNLGYEALFPPEMADVNPAILAALSPNADENHDFFSGSGSSYV 305 Query: 118 QGAELKWD 125 G ++ + Sbjct: 306 MGKTVETE 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 = 90.6 bits (224), Expect = 8e-20 Identities = 36/122 (29%), Positives = 67/122 (54%), Gaps = 9/122 (7%) Query: 1 MRDESLHLNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEATLLEIAYAHETMPKGFVGL 60 RDE LH +F + + ++ + P + + EA +E ++ E++P +G+ Sbjct: 223 SRDEGLHTDFNCLIYSLLENKLPENVVQNIVK-------EAVEVERSFICESLPCDLIGM 275 Query: 61 NAPSCEQYMQFIANRRCHQIGLEPLFKYTENPFPWMSEVIDLKKEKNFFETRVTEYQQGA 120 N+ QY++F+A+R +G +F ++NPF WM ++I L+ + NFFE RV +YQ+ Sbjct: 276 NSRLMSQYIEFVADRLLECLGCSKVFH-SKNPFNWM-DLISLQGKTNFFEKRVADYQKSG 333 Query: 121 EL 122 + Sbjct: 334 VM 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 = 89.9 bits (222), Expect = 1e-19 Identities = 38/128 (29%), Positives = 65/128 (50%), Gaps = 3/128 (2%) Query: 1 MRDESLHLNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEATLLEIAYAHETMPKGFVGL 60 RDE LH+ ++ ++ +E P L T+E + +T L +A LE + + G+ Sbjct: 217 NRDEQLHVYLFTNIFKELLVEFPELNTEETKTFVKTTLMKAADLEKDWFRYIIGDKIPGI 276 Query: 61 NAPSCEQYMQFIANRRCHQIGLEPLF-KYTENPFPWMSEVIDLKKEK-NFFETRVTEYQQ 118 N E Y+ FIAN+R Q+G+E + + NP W+ D+ K +FFE + +Y + Sbjct: 277 NPEDMETYISFIANKRAVQLGMEKPYPEIKHNPMKWIRAYEDVNSGKSDFFEQKSRQYAK 336 Query: 119 G-AELKWD 125 A+ +D Sbjct: 337 VSADNGFD 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 = 76.3 bits (187), Expect = 2e-15 Identities = 19/97 (19%), Positives = 43/97 (44%), Gaps = 4/97 (4%) Query: 1 MRDESLHLNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEATLLEIAYAHETMPKGFVGL 60 +RDES+H + Q + +E++ + ++++ EI Y + +G Sbjct: 198 IRDESVHGYYIGYKYQQGVKKLSEAEQEEYKAYTFDLMYDLYENEIEYTEDIYDD--LGW 255 Query: 61 NAPSCEQYMQFIANRRCHQIGLEPLFKYTENPF-PWM 96 ++++++ AN+ + +G E LF E P + Sbjct: 256 TE-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 = 75.2 bits (184), Expect = 3e-15 Identities = 26/96 (27%), Positives = 50/96 (52%), Gaps = 8/96 (8%) Query: 1 MRDESLHLNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEATLLEIAYAHETMPKGFVGL 60 RDE LH +F + + ++ + P + ++ EA +E ++ E++P +G+ Sbjct: 222 SRDEGLHTDFNCLIYSLLENKLPEEVVQN-------IVKEAVEVERSFICESLPCDLIGM 274 Query: 61 NAPSCEQYMQFIANRRCHQIGLEPLFKYTENPFPWM 96 N+ QY++F+A+R +G +F +NPF WM Sbjct: 275 NSRLMSQYIEFVADRLLECLGSPKIFH-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 = 69.3 bits (169), Expect = 2e-13 Identities = 14/112 (12%), Positives = 35/112 (31%), Gaps = 7/112 (6%) Query: 1 MRDESLHLNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEATLLEIAYAHETMPKGFVGL 60 DE H+ +G + + W F+ + ++ A L + L Sbjct: 208 GDDERRHMAWGTFTCRRHVAADDANW-TVFETRMNELIPLALRLIEEGFALYGDQPPFDL 266 Query: 61 NAPSCEQYMQFIANRRCHQIGLEPLFKYTENPFPWMS-EVIDLKKEKNFFET 111 + ++Q+ ++ + G + P + + + E F + Sbjct: 267 SKDD---FLQYSTDKGMRRFGTISNAR--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 = 28.8 bits (64), Expect = 0.32 Identities = 20/144 (13%), Positives = 44/144 (30%), Gaps = 49/144 (34%) Query: 1 MRDESLH---LNFGIDVINQIKIENP-HLWTKEFQQKSRTMLHEATLLEIAYAHETMPKG 56 R +L L + V P + Q + + L E +G Sbjct: 6 TRPLTLSHGSLEHVLLV--------PTASFFIASQLQEQ---FNKILPEPT-------EG 47 Query: 57 FVGLNAPS-----CEQYMQFIANRRC-HQIG-----LEPLFKYTENPFPWMSEV------ 99 F + P+ +++ ++++ ++G L EN + +++ Sbjct: 48 FAADDEPTTPAELVGKFLGYVSSLVEPSKVGQFDQVLNLCLTEFENCYLEGNDIHALAAK 107 Query: 100 --------IDLKKE--KNFFETRV 113 + KE KN+ R+ Sbjct: 108 LLQENDTTLVKTKELIKNYITARI 131 Score = 25.3 bits (55), Expect = 4.0 Identities = 12/84 (14%), Positives = 22/84 (26%), Gaps = 45/84 (53%) Query: 11 GIDVINQIKIENPHLWTKEFQQKSRTMLHEATLLEIAYAHETMP-KGFVGLNAP-SCE-- 66 G++++ W L P K ++ L+ P SC Sbjct: 212 GLNILE---------W-----------LENP---------SNTPDKDYL-LSIPISCPLI 241 Query: 67 ------QYMQFIANRRCHQIGLEP 84 Y+ + +G P Sbjct: 242 GVIQLAHYV--VT---AKLLGFTP 260 >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 = 26.3 bits (57), Expect = 1.9 Identities = 24/84 (28%), Positives = 30/84 (35%), Gaps = 30/84 (35%) Query: 8 LNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEA----------TLLE----------IA 47 LN G+ + P L KEF K R L E T LE A Sbjct: 727 LNGGLQFV-------PEL--KEFTAKLRKELVETSEVRKAVSIETALEHKVVNGNSADAA 777 Query: 48 YAH-ETMPKGFVGLNAPSCEQYMQ 70 YA E P+ + L+ P + Y Q Sbjct: 778 YAQVEIQPRANIQLDFPELKPYKQ 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 = 25.7 bits (55), Expect = 2.6 Identities = 7/25 (28%), Positives = 14/25 (56%), Gaps = 6/25 (24%) Query: 31 QQKSRTMLHEATL-LEIAYAHETMP 54 +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 = 25.3 bits (55), Expect = 4.3 Identities = 12/34 (35%), Positives = 13/34 (38%), Gaps = 1/34 (2%) Query: 11 GIDVINQIKIENPHLWTKEFQQKSRTMLHEATLL 44 + KIEN L K F K M E LL Sbjct: 30 NFKIEKIKKIENSELLDK-FTWKKSQMKEEGKLL 62 >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 = 6.2 Identities = 12/48 (25%), Positives = 25/48 (52%) Query: 8 LNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEATLLEIAYAHETMPK 55 +NFG+ + + E H W +E ++SR ++ + T +I + +T Sbjct: 117 MNFGLYPMLERFKEFAHGWEREHLERSRDLVFKNTFADIEFILKTCGG 164 >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 = 24.0 bits (52), Expect = 8.6 Identities = 6/11 (54%), Positives = 9/11 (81%) Query: 1 MRDESLHLNFG 11 ++DE HLN+G Sbjct: 155 VKDEYTHLNYG 165 >3lyh_A Cobalamin (vitamin B12) biosynthesis CBIX protein; structural genomics, joint center for structural genomics, JCSG; HET: MSE; 1.60A {Marinobacter aquaeolei} Length = 126 Score = 24.0 bits (52), Expect = 9.7 Identities = 10/62 (16%), Positives = 23/62 (37%), Gaps = 1/62 (1%) Query: 56 GFVGLNAPSCEQYMQFIANRRCHQIGLEPLFKYTENPFPW-MSEVIDLKKEKNFFETRVT 114 ++ L PS + + + Q + PLF + +I+ + ++ R+ Sbjct: 41 AYMELAEPSLDTIVNRAKGQGVEQFTVVPLFLAAGRHLRKDVPAMIERLEAEHGVTIRLA 100 Query: 115 EY 116 E Sbjct: 101 EP 102 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 0.135 0.421 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: 1,086,026 Number of extensions: 44129 Number of successful extensions: 144 Number of sequences better than 10.0: 1 Number of HSP's gapped: 118 Number of HSP's successfully gapped: 30 Length of query: 125 Length of database: 5,693,230 Length adjustment: 81 Effective length of query: 44 Effective length of database: 3,729,466 Effective search space: 164096504 Effective search space used: 164096504 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: 51 (24.0 bits)