RPS-BLAST 2.2.22 [Sep-27-2009]
Database: pdb70
24,244 sequences; 5,693,230 total letters
Searching..................................................done
Query= gi|254780136|ref|YP_003064549.1| 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)