RPS-BLAST 2.2.22 [Sep-27-2009] Database: mmdb70 33,805 sequences; 4,956,049 total letters Searching..................................................done Query= gi|254781006|ref|YP_003065419.1| ribonucleotide-diphosphate reductase subunit beta [Candidatus Liberibacter asiaticus str. psy62] (125 letters) >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} (A:150-346) Length = 197 Score = 118 bits (296), Expect = 3e-28 Identities = 38/128 (29%), Positives = 63/128 (49%), Gaps = 3/128 (2%) Query: 1 MRDESLHLNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEATLLEIAYAHETMPKGFVGL 60 RDE LH+ ++ ++ +E P L T+E + +T L +A LE + + G+ Sbjct: 68 NRDEQLHVYLFTNIFKELLVEFPELNTEETKTFVKTTLXKAADLEKDWFRYIIGDKIPGI 127 Query: 61 NAPSCEQYMQFIANRRCHQIGLEPLFK-YTENPFPWMSEVIDLKKEK-NFFETRVTEYQQ 118 N E Y+ FIAN+R Q+G E + NP W+ D+ K +FFE + +Y + Sbjct: 128 NPEDXETYISFIANKRAVQLGXEKPYPEIKHNPXKWIRAYEDVNSGKSDFFEQKSRQYAK 187 Query: 119 G-AELKWD 125 A+ +D Sbjct: 188 VSADNGFD 195 >1r2f_A Protein (ribonucleotide reductase R2); nucleotide metabolism, oxidoreductase; 2.10A {Salmonella typhimurium} (A:129-319) Length = 191 Score = 114 bits (286), Expect = 5e-27 Identities = 23/129 (17%), Positives = 45/129 (34%), Gaps = 7/129 (5%) Query: 1 MRDESLHLNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEATLLEIAYAHETMPKGFVGL 60 +RDE++H + + + +E + + +L E EI Y Sbjct: 61 IRDEAVHGYYIGYKYQIALQKLSAIEREELKLFALDLLMELYDNEIRYTEALYA---ETG 117 Query: 61 NAPSCEQYMQFIANRRCHQIGLEPLFKYTE---NPFPWMSEVIDLKKEKNFFETRVTEYQ 117 + ++ + AN+ +G E LF NP + + + +FF + Y Sbjct: 118 WVNDVKAFLCYNANKALMNLGYEALFPPEMADVNPAILAALSPNADENHDFFSGSGSSYV 177 Query: 118 QGAEL-KWD 125 G + D Sbjct: 178 MGKTVETED 186 >1syy_A Ribonucleoside-diphosphate reductase beta chain; DIIRON, oxygen activation, iron coupled radical, immune evasion, replication; 1.70A {Chlamydia trachomatis} (A:) Length = 346 Score = 111 bits (277), Expect = 4e-26 Identities = 71/124 (57%), Positives = 91/124 (73%), 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 RASMFIDYVQHIADRRLERIGLKPIY-HTKNPFPWMSETIDLNKEKNFFETRVIEYQHAA 342 Query: 121 ELKW 124 L W Sbjct: 343 SLTW 346 >3dhz_A Ribonucleotide reductase subunit R2F; metal free, hydrogen bond, metal binding protein; 1.63A {Corynebacterium ammoniagenes} (A:139-329) Length = 191 Score = 110 bits (277), Expect = 5e-26 Identities = 25/129 (19%), Positives = 53/129 (41%), Gaps = 7/129 (5%) Query: 1 MRDESLHLNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEATLLEIAYAHETMPKGFVGL 60 +RDES+H + Q + +E++ + ++++ EI Y + Sbjct: 61 IRDESVHGYYIGYKYQQGVKKLSEAEQEEYKAYTFDLMYDLYENEIEYTEDIYDDLG--- 117 Query: 61 NAPSCEQYMQFIANRRCHQIGLEPLF---KYTENPFPWMSEVIDLKKEKNFFETRVTEYQ 117 ++++++ AN+ + +G E LF + +P S + + +FF + Y Sbjct: 118 WTEDVKRFLRYNANKALNNLGYEGLFPTDETKVSPAILSSLSPNADENHDFFSGSGSSYV 177 Query: 118 QG-AELKWD 125 G AE D Sbjct: 178 IGKAEDTTD 186 >1jk0_B RNR Y4, ribonucleoside-diphosphate reductase small chain 2; ribonucleotide reductase, oxidoreductase; 2.80A {Saccharomyces cerevisiae} (B:147-345) Length = 199 Score = 104 bits (261), Expect = 4e-24 Identities = 27/125 (21%), Positives = 56/125 (44%), Gaps = 9/125 (7%) Query: 1 MRDESLHLNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEATLLEIAYAHETMPKGFVGL 60 RD + +F + ++ + ++ ++ EA +E Y ++P G+ Sbjct: 71 CRDRGAYTDFSCLLFAHLRTKPNPKIIEK-------IITEAVEIEKEYYSNSLPVEKFGM 123 Query: 61 NAPSCEQYMQFIANRRCHQIGLEPLFKYTENPFPWMSEVIDLKKEKNFFETRVTEYQQGA 120 + S Y++F+A+ G E + NPF +M +V K FFE +V++YQ+ + Sbjct: 124 DLKSIHTYIEFVADGLLQGFGNEKYYN-AVNPFEFMEDVATAGK-TTFFEKKVSDYQKAS 181 Query: 121 ELKWD 125 ++ Sbjct: 182 DMSKS 186 >1jk0_A RNR Y2, ribonucleoside-diphosphate reductase small chain 1; ribonucleotide reductase, oxidoreductase; 2.80A {Saccharomyces cerevisiae} (A:1-103,A:228-419) Length = 295 Score = 103 bits (259), Expect = 7e-24 Identities = 35/124 (28%), Positives = 60/124 (48%), Gaps = 9/124 (7%) Query: 1 MRDESLHLNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEATLLEIAYAHETMPKGFVGL 60 RDE LH +F + +K + ++ ++ EA +E Y + +P +G+ Sbjct: 166 CRDEGLHTDFACLLFAHLKNKPDPAIVEK-------IVTEAVEIEQRYFLDALPVALLGM 218 Query: 61 NAPSCEQYMQFIANRRCHQIGLEPLFKYTENPFPWMSEVIDLKKEKNFFETRVTEYQQGA 120 NA QY++F+A+R G + + ENPF +M + K NFFE RV++YQ+ Sbjct: 219 NADLMNQYVEFVADRLLVAFGNKKYY-KVENPFDFMENISLAGK-TNFFEKRVSDYQKAG 276 Query: 121 ELKW 124 + Sbjct: 277 VMSK 280 >1h0o_A Ribonucleoside-diphosphate reductase; oxidoreductase, ribonucleotide reductase, dinuclear metal-cluster; 2.2A {Mus musculus} (A:219-390) Length = 172 Score = 101 bits (252), Expect = 5e-23 Identities = 36/125 (28%), Positives = 60/125 (48%), Gaps = 9/125 (7%) Query: 1 MRDESLHLNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEATLLEIAYAHETMPKGFVGL 60 RDE LH +F + + + +E ++ A +E + E +P +G+ Sbjct: 46 SRDEGLHCDFACLMFKHLVHKPAEQRVRE-------IITNAVRIEQEFLTEALPVKLIGM 98 Query: 61 NAPSCEQYMQFIANRRCHQIGLEPLFKYTENPFPWMSEVIDLKKEKNFFETRVTEYQQGA 120 N +QY++F+A+R ++G ENPF +M E I L+ + NFFE RV EYQ+ Sbjct: 99 NCTLMKQYIEFVADRLMLELGFNK-IFRVENPFDFM-ENISLEGKTNFFEKRVGEYQRMG 156 Query: 121 ELKWD 125 + Sbjct: 157 VMSNS 161 >1mxr_A Ribonucleotide reductase R2; radical protein, DI iron, oxidoreductase; 1.42A {Escherichia coli} (A:) Length = 375 Score = 99.5 bits (247), Expect = 1e-22 Identities = 32/126 (25%), Positives = 55/126 (43%), Gaps = 6/126 (4%) Query: 1 MRDESLHLNFGIDVINQIKIENPHLWT----KEFQQKSRTMLHEATLLEIAYAHETMPKG 56 RDE+LHL ++N ++ +E +Q+ + +A E +A G Sbjct: 235 ARDEALHLTGTQHMLNLLRSGADDPEMAEIAEECKQECYDLFVQAAQQEKDWADYLFRDG 294 Query: 57 -FVGLNAPSCEQYMQFIANRRCHQIGLEPLFKYTENPFPWMSEVIDLKKEK-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 >2p1i_A Ribonucleotide reductase, small chain; F222 twinning, plasmodb PY03671, structural genomics consortium, SGC, oxidoreductase; 2.70A {Plasmodium yoelii yoelii str} (A:162-349) Length = 188 Score = 98.9 bits (246), Expect = 2e-22 Identities = 36/125 (28%), Positives = 68/125 (54%), Gaps = 9/125 (7%) Query: 1 MRDESLHLNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEATLLEIAYAHETMPKGFVGL 60 RDE LH +F + + ++ + P + ++ EA +E ++ E++P +G+ Sbjct: 62 SRDEGLHTDFNCLIYSLLENKLPENVVQN-------IVKEAVEVERSFICESLPCDLIGM 114 Query: 61 NAPSCEQYMQFIANRRCHQIGLEPLFKYTENPFPWMSEVIDLKKEKNFFETRVTEYQQGA 120 N+ QY++F+A+R +G +F ++NPF WM ++I L+ + NFFE RV +YQ+ Sbjct: 115 NSRLMSQYIEFVADRLLECLGCSKVFH-SKNPFNWM-DLISLQGKTNFFEKRVADYQKSG 172 Query: 121 ELKWD 125 + Sbjct: 173 VMAQR 177 >2o1z_A Ribonucleotide reductase subunit R2; small subunit ribonucleotide reductase, oxidoreductase, DNA replication, iron, DIIRON, radical, R2 subunit; 2.40A {Plasmodium vivax} (A:161-311) Length = 151 Score = 86.5 bits (214), Expect = 1e-18 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: 62 SRDEGLHTDFNCLIYSLLENKLPEEVVQN-------IVKEAVEVERSFICESLPCDLIGM 114 Query: 61 NAPSCEQYMQFIANRRCHQIGLEPLFKYTENPFPWM 96 N+ QY++F+A+R +G +F +NPF WM Sbjct: 115 NSRLMSQYIEFVADRLLECLGSPKIFH-AKNPFNWM 149 >3ee4_A Probable ribonucleoside-diphosphate reductase; manganese, iron, DIIRON, carboxylate, oxidase, ligand, cavity, monooxygenase; HET: MYR; 1.90A {Mycobacterium tuberculosis} (A:) Length = 323 Score = 81.8 bits (201), Expect = 3e-17 Identities = 16/120 (13%), Positives = 30/120 (25%), Gaps = 5/120 (4%) Query: 1 MRDESLHLNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEATLLEIAYAHETMPKGFVGL 60 DE H+ +G + + W F+ + ++ A L + L Sbjct: 208 GDDERRHMAWGTFTCRRHVAADDANW-TVFETRMNELIPLALRLIEEGFALYGDQPPFDL 266 Query: 61 NAPSCEQYMQFIANRRCHQIGLEPLFKYTENPFPWMSEVIDLKKEKNFFETRVTEYQQGA 120 + QY RR I + + E F + + Sbjct: 267 SKDDFLQYSTDKGMRRFGTISNARGR----PVAEIDVDYSPAQLEDTFADEDRRTLAAAS 322 >3chh_A P-aminobenzoate N-oxygenase; DI-iron oxygenase, oxidoreductase; 2.00A {Streptomyces thioluteus} PDB: 3chi_A 3cht_A* 3chu_A 2jcd_A (A:) Length = 336 Score = 60.3 bits (145), Expect = 8e-11 Identities = 10/111 (9%), Positives = 31/111 (27%), Gaps = 11/111 (9%) Query: 1 MRDESLHLNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEATLLEIAYAHETMPKGFVGL 60 +RDE+ H + ++V+ ++ + + L +++ + G+ Sbjct: 224 LRDETAHGSIVVEVVRELYARMNEQQRRALVRCLPIALEAFAEQDLSALLLELNA--AGI 281 Query: 61 NAPSC-EQYMQFIANRRCHQIGLEPLFKYTENPFPWMSEVIDLKKEKNFFE 110 ++ A + + + L +F Sbjct: 282 RGAEEIVGDLRSTAGGTRLVRDFSG-------ARKMVEQ-LGLDDAVDFDF 324 >3fho_A ATP-dependent RNA helicase DBP5; mRNA export, ATPase, translation termination, ATP-binding, cytoplasm, hydrolase, membrane; 2.80A {Schizosaccharomyces pombe} (A:1-326) Length = 326 Score = 26.3 bits (57), Expect = 1.5 Identities = 8/54 (14%), Positives = 17/54 (31%), Gaps = 9/54 (16%) Query: 3 DESLHLNFGIDVINQIKIENPH-----L----WTKEFQQKSRTMLHEATLLEIA 47 D L D +IK P L +++ ++ + A + + Sbjct: 269 DNMLDQQGLGDQSMRIKHLLPRNTQIVLFSATFSERVEKYAERFAPNANEIRLK 322 >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} (A:) Length = 244 Score = 24.4 bits (53), Expect = 4.9 Identities = 12/41 (29%), Positives = 16/41 (39%), Gaps = 12/41 (29%) Query: 1 MRDESLHLNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEA 41 ++DE HLN+G W K + R L EA Sbjct: 155 VKDEYTHLNYG------------EAWLKANLESCREELLEA 183 >3hn3_A Beta-G1, beta-glucuronidase; lysosomal enzyme, acid hydrolase, glycosidase, alternative splicing, disease mutation, glycoprotein, hydrolase; HET: NDG NAG BMA MAN GUP; 1.70A {Homo sapiens} PDB: 1bhg_A* (A:206-306) Length = 101 Score = 24.5 bits (53), Expect = 5.5 Identities = 3/21 (14%), Positives = 8/21 (38%) Query: 9 NFGIDVINQIKIENPHLWTKE 29 G + + + P+L + Sbjct: 51 TQGQLKVPGVSLWWPYLMHER 71 >2odr_A Phosphoseryl-tRNA synthetase; phosphoserine tRNA synthetase class II, ligase; 3.23A {Methanococcus maripaludis S2} (A:550-614) Length = 65 Score = 24.3 bits (52), Expect = 5.6 Identities = 4/7 (57%), Positives = 6/7 (85%), Gaps = 1/7 (14%) Query: 16 N-QIKIE 21 N ++KIE Sbjct: 1 NVEVKIE 7 >2odr_B Phosphoseryl-tRNA synthetase; phosphoserine tRNA synthetase class II, ligase; 3.23A {Methanococcus maripaludis S2} (B:550-611) Length = 62 Score = 23.9 bits (51), Expect = 7.2 Identities = 4/7 (57%), Positives = 6/7 (85%), Gaps = 1/7 (14%) Query: 16 N-QIKIE 21 N ++KIE Sbjct: 1 NVEVKIE 7 Database: mmdb70 Posted date: Jun 20, 2010 3:12 AM Number of letters in database: 4,956,049 Number of sequences in database: 33,805 Lambda K H 0.321 0.135 0.421 Gapped Lambda K H 0.267 0.0714 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 33805 Number of Hits to DB: 952,230 Number of extensions: 37144 Number of successful extensions: 120 Number of sequences better than 10.0: 1 Number of HSP's gapped: 94 Number of HSP's successfully gapped: 24 Length of query: 125 Length of database: 4,956,049 Length adjustment: 75 Effective length of query: 50 Effective length of database: 2,420,674 Effective search space: 121033700 Effective search space used: 121033700 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: 50 (23.1 bits)