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)