RPS-BLAST 2.2.22 [Sep-27-2009] Database: mmdb70 33,805 sequences; 4,956,049 total letters Searching..................................................done Query= 537021.9.peg.74_1 (196 letters) >1h0o_A Ribonucleoside-diphosphate reductase; oxidoreductase, ribonucleotide reductase, dinuclear metal-cluster; 2.2A {Mus musculus} (A:1-218) Length = 218 Score = 148 bits (374), Expect = 5e-37 Identities = 44/156 (28%), Positives = 73/156 (46%), Gaps = 6/156 (3%) Query: 15 KRVNVDDKRMLNARSDVNQLLPLKYGWAWEKYLSACNNHWMPTEVPMQDDLALWKSKNGL 74 +V+D+ +L + P++Y W+ Y A + W EV + D+ W++ L Sbjct: 64 TNPSVEDEPLLRENPRRFVVFPIEYHDIWQMYKKAEASFWTAEEVDLSKDIQHWEA---L 120 Query: 75 TDDERLMIKRNLGFFASSESLVANNIVLAIYRHLSNPECRQYLLRQAFEEAVHSHTFQYI 134 DER I L FFA+S+ +V N+V + + E R + Q E +HS + + Sbjct: 121 KPDERHFISHVLAFFAASDGIVNENLVERFSQEVQVTEARCFYGFQIAMENIHSEMYSLL 180 Query: 135 ITSLGLDEGE---LFNMYREVPSITAKANWALQYTQ 167 I + D E LFN +P + KA+WAL++ Sbjct: 181 IDTYIKDPKEREYLFNAIETMPCVKKKADWALRWIG 216 >1mxr_A Ribonucleotide reductase R2; radical protein, DI iron, oxidoreductase; 1.42A {Escherichia coli} (A:) Length = 375 Score = 143 bits (361), Expect = 2e-35 Identities = 31/182 (17%), Positives = 71/182 (39%), Gaps = 4/182 (2%) Query: 14 EKRVNVDDKRMLNARS-DVNQLLPLKYGWAWEKYLSACNNHWMPTEVPMQDDLALWKSKN 72 + + + + M + +V + KY + + W P EV + D +++ Sbjct: 7 QTKNDQLKEPMFFGQPVNVARYDQQKYDIFEKLIEKQLSFFWRPEEVDVSRDRIDYQA-- 64 Query: 73 GLTDDERLMIKRNLGFFASSESLVANNIVLAIYRHLSNPECRQYLLRQAFEEAVHSHTFQ 132 L + E+ + NL + +S+ + +A+ +S PE ++ AF E +HS ++ Sbjct: 65 -LPEHEKHIFISNLKYQTLLDSIQGRSPNVALLPLISIPELETWVETWAFSETIHSRSYT 123 Query: 133 YIITSLGLDEGELFNMYREVPSITAKANWALQYTQTLSSPSFHYWNKRRRSRILTRSLRF 192 +II ++ D +F+ I +A Y L + ++ + + Sbjct: 124 HIIRNIVNDPSVVFDDIVTNEQIQKRAEGISSYYDELIEMTSYWHLLGEGTHTVNGKTVT 183 Query: 193 LC 194 + Sbjct: 184 VS 185 >2p1i_A Ribonucleotide reductase, small chain; F222 twinning, plasmodb PY03671, structural genomics consortium, SGC, oxidoreductase; 2.70A {Plasmodium yoelii yoelii str} (A:1-161) Length = 161 Score = 141 bits (357), Expect = 5e-35 Identities = 40/164 (24%), Positives = 73/164 (44%), Gaps = 12/164 (7%) Query: 1 MANNTGLSPIQA---------GEKRVNVDDKRMLNARSDVNQLLPLKYGWAWEKYLSACN 51 MA +S + ++ ++++LN S+ L P+ Y W Y A Sbjct: 1 MAEVVNISKSASFSKQEKEFSDFQKSKESNEKILNKESNRFTLHPIMYPEVWNFYKKAEA 60 Query: 52 NHWMPTEVPMQDDLALWKSKNGLTDDERLMIKRNLGFFASSESLVANNIVLAIYRHLSNP 111 + W E+ + DL ++ L +E+ IK L FFA+S+ +V N+ R + Sbjct: 61 SFWTAEEIDLSSDLKDFEK---LNVNEKHFIKHVLAFFAASDGIVLENLASKFLREVEII 117 Query: 112 ECRQYLLRQAFEEAVHSHTFQYIITSLGLDEGELFNMYREVPSI 155 E +++ Q E +HS T+ +I + DE E N++ + +I Sbjct: 118 EAKKFYSFQIAVENIHSETYSLLIDNYIKDEKERLNLFHAIENI 161 >1syy_A Ribonucleoside-diphosphate reductase beta chain; DIIRON, oxygen activation, iron coupled radical, immune evasion, replication; 1.70A {Chlamydia trachomatis} (A:) Length = 346 Score = 134 bits (337), Expect = 9e-33 Identities = 95/183 (51%), Positives = 131/183 (71%), Gaps = 2/183 (1%) Query: 9 PIQAGEKRVNVDDKRMLNARS-DVNQLLPLKYGWAWEKYLSACNNHWMPTEVPMQDDLAL 67 + +KRVN++ KR++N DVNQL+P+KY WAWE YL+ C N+W+PTE+PM D+ L Sbjct: 5 ILDGKQKRVNLNSKRLVNCNQVDVNQLVPIKYKWAWEHYLNGCANNWLPTEIPMGKDIEL 64 Query: 68 WKSKNGLTDDERLMIKRNLGFFASSESLVANNIVLAIYRHLSNPECRQYLLRQAFEEAVH 127 WKS + L++DER +I NLGFF+++ESLV NNIVLAI++H++NPE RQYLLRQAFEEAVH Sbjct: 65 WKS-DRLSEDERRVILLNLGFFSTAESLVGNNIVLAIFKHVTNPEARQYLLRQAFEEAVH 123 Query: 128 SHTFQYIITSLGLDEGELFNMYREVPSITAKANWALQYTQTLSSPSFHYWNKRRRSRILT 187 +HTF YI SLGLDE E+FN Y E +I AK ++ ++ T + P+F + + Sbjct: 124 THTFLYICESLGLDEKEIFNAYNERAAIKAKDDFQMEITGKVLDPNFRTDSVEGLQEFVK 183 Query: 188 RSL 190 + Sbjct: 184 NLV 186 >1jk0_A RNR Y2, ribonucleoside-diphosphate reductase small chain 1; ribonucleotide reductase, oxidoreductase; 2.80A {Saccharomyces cerevisiae} (A:104-227) Length = 124 Score = 130 bits (327), Expect = 2e-31 Identities = 34/123 (27%), Positives = 60/123 (48%), Gaps = 2/123 (1%) Query: 33 QLLPLKYGWAWEKYLSACNNHWMPTEVPMQDDLALWKSKNGLTDDERLMIKRNLGFFASS 92 L P+KY W+ Y A + W E+ + D+ W ++ + ++ER I R L FFA+S Sbjct: 4 VLFPIKYHEIWQAYKRAEASFWTAEEIDLSKDIHDWNNR--MNENERFFISRVLAFFAAS 61 Query: 93 ESLVANNIVLAIYRHLSNPECRQYLLRQAFEEAVHSHTFQYIITSLGLDEGELFNMYREV 152 + +V N+V + PE + + Q E +HS T+ +I + D E ++ + Sbjct: 62 DGIVNENLVENFSTEVQIPEAKSFYGFQIMIENIHSETYSLLIDTYIKDPKESEFLFNAI 121 Query: 153 PSI 155 +I Sbjct: 122 HTI 124 >2o1z_A Ribonucleotide reductase subunit R2; small subunit ribonucleotide reductase, oxidoreductase, DNA replication, iron, DIIRON, radical, R2 subunit; 2.40A {Plasmodium vivax} (A:38-160) Length = 123 Score = 125 bits (315), Expect = 4e-30 Identities = 35/123 (28%), Positives = 60/123 (48%), Gaps = 3/123 (2%) Query: 33 QLLPLKYGWAWEKYLSACNNHWMPTEVPMQDDLALWKSKNGLTDDERLMIKRNLGFFASS 92 L P+ Y W+ Y A + W E+ + DL ++ L D+E+ IK L FFA+S Sbjct: 4 TLYPILYPDVWDFYKKAEASFWTAEEIDLSSDLKDFEK---LNDNEKHFIKHVLAFFAAS 60 Query: 93 ESLVANNIVLAIYRHLSNPECRQYLLRQAFEEAVHSHTFQYIITSLGLDEGELFNMYREV 152 + +V N+ R + E +++ Q E +HS T+ +I + DE E N++ + Sbjct: 61 DGIVLENLASKFLRQVKITEAKKFYAFQIAVENIHSETYSLLIDNYIKDEKERMNLFHAI 120 Query: 153 PSI 155 +I Sbjct: 121 ENI 123 >1r2f_A Protein (ribonucleotide reductase R2); nucleotide metabolism, oxidoreductase; 2.10A {Salmonella typhimurium} (A:1-128) Length = 128 Score = 123 bits (311), Expect = 1e-29 Identities = 23/130 (17%), Positives = 51/130 (39%), Gaps = 5/130 (3%) Query: 24 MLNARSDVNQLLPLKYGWAWEKYLSACNNHWMPTEVPMQDDLALWKSKNGLTDDERLMIK 83 M +R ++ E + +N W+P +VP+ +D+ W++ L+ E+ + Sbjct: 1 MKLSRISAINWNKIQDDKDLEVWNRLTSNFWLPEKVPLSNDIPAWQT---LSAAEQQLTI 57 Query: 84 RNLGFFASSESLVANNIVLAIYRHLSNPECRQYLLRQAFEEAVHSHTFQYIITSLGLDE- 142 R +++ ++ P L +F EAVH+ ++ I ++L + Sbjct: 58 RVFTGLTLLDTIQNIAGAPSLMADAITPHEEAVLSNISFMEAVHARSYSSIFSTLCQTKE 117 Query: 143 -GELFNMYRE 151 + E Sbjct: 118 VDAAYAWSEE 127 >1jk0_B RNR Y4, ribonucleoside-diphosphate reductase small chain 2; ribonucleotide reductase, oxidoreductase; 2.80A {Saccharomyces cerevisiae} (B:33-146) Length = 114 Score = 120 bits (302), Expect = 1e-28 Identities = 26/111 (23%), Positives = 47/111 (42%), Gaps = 3/111 (2%) Query: 34 LLPLKYGWAWEKYLSACNNHWMPTEVPMQDDLALWKSKNGLTDDERLMIKRNLGFFASSE 93 + P+KY W Y + W E+ + D ++ LTDD++ I L SS+ Sbjct: 5 MFPIKYHEIWAAYKKVEASFWTAEEIELAKDTEDFQK---LTDDQKTYIGNLLALSISSD 61 Query: 94 SLVANNIVLAIYRHLSNPECRQYLLRQAFEEAVHSHTFQYIITSLGLDEGE 144 +LV ++ L NPE + + Q E ++S + ++ + D Sbjct: 62 NLVNKYLIENFSAQLQNPEGKSFYGFQIMMENIYSEVYSMMVDAFFKDPKN 112 >3dhz_A Ribonucleotide reductase subunit R2F; metal free, hydrogen bond, metal binding protein; 1.63A {Corynebacterium ammoniagenes} (A:21-138) Length = 118 Score = 117 bits (295), Expect = 1e-27 Identities = 21/117 (17%), Positives = 42/117 (35%), Gaps = 5/117 (4%) Query: 37 LKYGWAWEKYLSACNNHWMPTEVPMQDDLALWKSKNGLTDDERLMIKRNLGFFASSESLV 96 + E + N W+P ++P+ +D+ W +T E+L R +++ Sbjct: 4 IPDEKDLEVWDRLTGNFWLPEKIPVSNDIQSWNK---MTPQEQLATMRVFTGLTLLDTIQ 60 Query: 97 ANNIVLAIYRHLSNPECRQYLLRQAFEEAVHSHTFQYIITSLGLDEG--ELFNMYRE 151 +++ AF E+VH+ ++ I +L E F E Sbjct: 61 GTVGAISLLPDAETMHEEAVYTNIAFMESVHAKSYSNIFMTLASTPQINEAFRWSEE 117 >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:1-149) Length = 149 Score = 114 bits (287), Expect = 8e-27 Identities = 29/141 (20%), Positives = 63/141 (44%), Gaps = 7/141 (4%) Query: 14 EKRVNVDDKRMLNAR-SDVNQLLPLKYGWAWEKYLSACNNHWMPTEVPMQDDLALWKSKN 72 + + +LN + S+V +++ WA+ Y + N W P E+ D + + Sbjct: 12 DTTASNASTGILNGKSSNVLNWDDVRFSWAYPLYKNXLANFWTPFEINXSHDAKQFPT-- 69 Query: 73 GLTDDERLMIKRNLGFFASSESLVANNIVLAIYRHLSNPECRQYLLRQAFEEAVHSHTFQ 132 LT+ E+ K+ +G A +S+ + +L++ +F+E VH+ ++ Sbjct: 70 -LTETEQEAFKKIIGLLAFLDSVQTDYSX-RAAEYLTDSSLAALXSVLSFQEVVHNQSYS 127 Query: 133 YIITSLGLDE--GELFNMYRE 151 Y+++SL E+F ++ Sbjct: 128 YVLSSLVPKATQDEIFEYWKH 148 >3ee4_A Probable ribonucleoside-diphosphate reductase; manganese, iron, DIIRON, carboxylate, oxidase, ligand, cavity, monooxygenase; HET: MYR; 1.90A {Mycobacterium tuberculosis} (A:) Length = 323 Score = 104 bits (260), Expect = 8e-24 Identities = 30/161 (18%), Positives = 55/161 (34%), Gaps = 13/161 (8%) Query: 7 LSPIQAGEKRVNVDDKRMLNARSDVNQLLPLKYGWAWEKYLSACNNHWMPTEVPMQDDLA 66 ++ + + + + W P ++ D A Sbjct: 1 MAHHHHHHGMTRTRSGSLAAGGLNWAS-------LPLKLFAGGNAKFWHPADIDFTRDRA 53 Query: 67 LWKSKNGLTDDERLMIKRNLGFFASSESLVANNI--VLAIYRHLSNPECRQYLLRQAFEE 124 W+ L+DDER R F + E V +I ++ R YL + AFEE Sbjct: 54 DWEK---LSDDERDYATRLCTQFIAGEEAVTEDIQPFMSAMRAEGRLADEMYLTQFAFEE 110 Query: 125 AVHSHTFQYIITSLGLDEGELFNMYREVPSITAKANWALQY 165 A H+ F+ + ++G+ E +L ++P+ L Sbjct: 111 AKHTQVFRMWLDAVGISE-DLHRYLDDLPAYRQIFYAELPE 150 >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 = 89.9 bits (222), Expect = 2e-19 Identities = 15/169 (8%), Positives = 46/169 (27%), Gaps = 23/169 (13%) Query: 15 KRVNVDDKRMLNARSDVNQLLPL--KYGWAWEKYLS-------ACNNHWMPTEVPMQDDL 65 R V+++ + +A + +L+ + K P E+ + Sbjct: 14 ARGWVEEEGIGSA--TLGRLVRAWPRRAAVVNKADILDEWADYDTLVPDYPLEIVPFAEH 71 Query: 66 ALWKSKNGLTDDERLMIKRNLGFFASSESLVANNIVLA---------IYRHLSNPECRQY 116 L+ +R + + + + ++ ++ +P R+ Sbjct: 72 PLF---LAAEPHQRQRVLTGMWIGYNERVIATEQLIAEPAFDLVMHGVFPGSDDPLIRKS 128 Query: 117 LLRQAFEEAVHSHTFQYIITSLGLDEGELFNMYREVPSITAKANWALQY 165 + + +E+ H++ I + + L Sbjct: 129 VQQAIVDESFHTYMHMLAIDRTRELRKISERPPQPELVTYRRLRRVLAD 177 >1mty_D Methane monooxygenase hydroxylase; dinuclear iron center monooxygenase; 1.70A {Methylococcus capsulatus str} (D:1-248) Length = 248 Score = 32.9 bits (75), Expect = 0.027 Identities = 14/101 (13%), Positives = 26/101 (25%), Gaps = 1/101 (0%) Query: 46 YLSACNNHWMPTEVPMQDDLALWKSKNGLTDDERLMIKRNLGFFASSESLVANNIVLAIY 105 Y +Q L + + +K F E A ++ Sbjct: 53 YARMEAVKDERQFGSLQVALTRLNAGVRVHPKWNETMKVVSNFLEVGE-YNAIAATGMLW 111 Query: 106 RHLSNPECRQYLLRQAFEEAVHSHTFQYIITSLGLDEGELF 146 E + L Q +E H+H Y+ + + Sbjct: 112 DSAQAAEQKNGYLAQVLDEIRHTHQCAYVNYYFAKNGQDPA 152 >1jk0_B RNR Y4, ribonucleoside-diphosphate reductase small chain 2; ribonucleotide reductase, oxidoreductase; 2.80A {Saccharomyces cerevisiae} (B:147-345) Length = 199 Score = 32.2 bits (73), Expect = 0.044 Identities = 5/23 (21%), Positives = 10/23 (43%) Query: 145 LFNMYREVPSITAKANWALQYTQ 167 LF +P + KA + ++ Sbjct: 1 LFKEIANLPEVKHKAAFIERWIS 23 >2e0z_A Virus-like particle; bacteriophage, HK97; 3.60A {Pyrococcus furiosus} (A:) Length = 345 Score = 30.3 bits (68), Expect = 0.17 Identities = 18/109 (16%), Positives = 34/109 (31%), Gaps = 6/109 (5%) Query: 76 DDERLMIKRNLGFFASSESLVANNIVLAIYRHLSNPECRQYLLRQAFEEAVHSHTFQYII 135 + + L +E A N+ + R+ + R+ LL A EE H F ++ Sbjct: 14 PYTKEELMEILRLAIIAEL-DAINLYEQMARYSEDENVRKILLDVAREEKAHVGEFMALL 72 Query: 136 TSLGLDEGELFNMYR-EVPSITAKANWALQYTQTLSSP----SFHYWNK 179 +L ++ EV +T + S+ Sbjct: 73 LNLDPEQVTELKGGFEEVKELTGIEAHINDNKKEESNVEYFEKLRSALL 121 >2wfo_A Glycoprotein 1, MACV-GP1; arenavirus, NEW world arenavirus, hemorrhagic fever virus, envelope protein, junin, guanarito, sabia, chapare, virion; HET: NAG; 1.73A {Machupo virus} (A:) Length = 182 Score = 27.9 bits (62), Expect = 1.1 Identities = 13/67 (19%), Positives = 23/67 (34%), Gaps = 12/67 (17%) Query: 118 LRQAFEEAVHSHTFQYIITSLGLDEGELFNMYREVPSI-----TAKANWALQYTQTLSSP 172 L ++ S + +LG D + M P + T K +Q+ + + Sbjct: 46 LGNCLNKSDSSWAIHWFSIALGHD----WLMD---PPMLCRNKTKKEGSNIQFNISKADE 98 Query: 173 SFHYWNK 179 S Y K Sbjct: 99 SRVYGKK 105 >1sw5_A Osmoprotection protein (PROX); binding-protein, compatible solutes, cation-PI interactions, non-classical hydrogen bonds; 1.80A {Archaeoglobus fulgidus dsm 4304} (A:1-110,A:209-275) Length = 177 Score = 26.3 bits (58), Expect = 3.2 Identities = 8/52 (15%), Positives = 17/52 (32%), Gaps = 3/52 (5%) Query: 5 TGLSPIQAGEKRVNVDDKRMLNARSDVNQLLPLKYGWAWEKYLSACNNHWMP 56 T + I + D + + + V + L G L ++ +P Sbjct: 66 TAYNVILRKQPPELWDQQYIFDE---VKKGLLEADGVVVAAKLGFRDDGALP 114 >1qap_A Quinolinic acid phosphoribosyltransferase; glycosyltransferase, NAD biosynthesis; HET: NTM; 2.80A {Salmonella typhimurium} (A:1-142,A:286-296) Length = 153 Score = 26.1 bits (57), Expect = 3.5 Identities = 6/63 (9%), Positives = 14/63 (22%), Gaps = 3/63 (4%) Query: 115 QYLLRQAFEEAVHSHTFQYIITSLGLDEGEL---FNMYREVPSITAKANWALQYTQTLSS 171 + QA E + + L + + + W + L+ Sbjct: 23 PAAVAQALREDLGGEVDAGNDITAQLLPADTQAHATVITREDGVFCGKRWVEEVFIQLAG 82 Query: 172 PSF 174 Sbjct: 83 DDV 85 >1uf2_A Core protein P3; virus components, icosahedral virus; 3.50A {Rice dwarf virus} (A:1-141,A:230-245,A:658-772,A:963-971) Length = 281 Score = 25.8 bits (56), Expect = 4.5 Identities = 9/23 (39%), Positives = 14/23 (60%) Query: 88 FFASSESLVANNIVLAIYRHLSN 110 FFA E ++ ++ A+Y LSN Sbjct: 162 FFAGGEDILILQLIRAVYDTLSN 184 >2fzf_A Hypothetical protein; structural genomics, southeast collaboratory for structural genomics, secsg, protein structure initiative, PSI; 2.70A {Pyrococcus furiosus} (A:1-90) Length = 90 Score = 25.6 bits (56), Expect = 4.6 Identities = 5/46 (10%), Positives = 16/46 (34%) Query: 97 ANNIVLAIYRHLSNPECRQYLLRQAFEEAVHSHTFQYIITSLGLDE 142 A ++ + ++ + A EE H + + + + + Sbjct: 35 AREFYKSLAEKIKIEALKEKINWLAEEEKKHEALLRKLYSQMFPGK 80 >3gvf_A Inorganic pyrophosphatase; structural genomics, hydrolase, seattle structural genomics center for infectious disease, ssgcid; HET: PGE; 1.75A {Burkholderia pseudomallei 1710B} PDB: 3d63_A* 3eiy_A 3ej0_A* 3ej2_A* 3eiz_A* (A:) Length = 196 Score = 24.8 bits (54), Expect = 7.5 Identities = 15/84 (17%), Positives = 28/84 (33%), Gaps = 11/84 (13%) Query: 110 NPECRQYLLRQAFEEAVHSHTFQYIITSLGLDEGELFNMYREVPS-------ITAKANWA 162 + L Q + S +F + G D + FN+ E+P+ KA Sbjct: 5 HHHHMGTLEAQ--TQGPGSMSFSNV--PAGKDLPQDFNVIIEIPAQSEPVKYEADKALGL 60 Query: 163 LQYTQTLSSPSFHYWNKRRRSRIL 186 L + + + + N + L Sbjct: 61 LVVDRFIGTGMRYPVNYGFIPQTL 84 >3caw_A O-succinylbenzoate synthase; structural genomics, PSI-2, NYSGXRC, target 9462A, protein structure initiative; 1.87A {Bdellovibrio bacteriovorus HD100} (A:96-310) Length = 215 Score = 24.7 bits (53), Expect = 8.3 Identities = 4/38 (10%), Positives = 7/38 (18%) Query: 30 DVNQLLPLKYGWAWEKYLSACNNHWMPTEVPMQDDLAL 67 D N L + + L + Sbjct: 60 DFNALGSWQTFEKFMVNLPLTVRPLIEYVEDPFPFDFH 97 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 0.133 0.411 Gapped Lambda K H 0.267 0.0613 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 33805 Number of Hits to DB: 1,517,667 Number of extensions: 64625 Number of successful extensions: 175 Number of sequences better than 10.0: 1 Number of HSP's gapped: 161 Number of HSP's successfully gapped: 28 Length of query: 196 Length of database: 4,956,049 Length adjustment: 84 Effective length of query: 112 Effective length of database: 2,116,429 Effective search space: 237040048 Effective search space used: 237040048 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: 52 (24.1 bits)