RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy7988
(73 letters)
>2p1i_A Ribonucleotide reductase, small chain; F222 twinning, plasmodb
PY03671, S genomics consortium, SGC, oxidoreductase;
2.70A {Plasmodium yoelii yoelii}
Length = 349
Score = 79.9 bits (197), Expect = 6e-20
Identities = 27/51 (52%), Positives = 40/51 (78%)
Query: 23 QHYFAENPFDFMENISLEGKTNFFERKVGEYQKSSVMADQDNQVFRLDEQF 73
+ + ++NPF++M+ ISL+GKTNFFE++V +YQKS VMA + QVF L+ F
Sbjct: 299 KVFHSKNPFNWMDLISLQGKTNFFEKRVADYQKSGVMAQRKEQVFSLNTDF 349
>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 = 79.6 bits (196), Expect = 1e-19
Identities = 31/51 (60%), Positives = 38/51 (74%)
Query: 23 QHYFAENPFDFMENISLEGKTNFFERKVGEYQKSSVMADQDNQVFRLDEQF 73
+ + ENPFDFMENISLEGKTNFFE++VGEYQ+ VM++ F LD F
Sbjct: 340 KIFRVENPFDFMENISLEGKTNFFEKRVGEYQRMGVMSNSTENSFTLDADF 390
>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 = 74.2 bits (182), Expect = 1e-17
Identities = 30/54 (55%), Positives = 39/54 (72%), Gaps = 3/54 (5%)
Query: 23 QHYFAENPFDFMENISLEGKTNFFERKVGEYQKSSVMA---DQDNQVFRLDEQF 73
++Y ENPFDFMENISL GKTNFFE++V +YQK+ VM+ Q+ F +E F
Sbjct: 366 KYYKVENPFDFMENISLAGKTNFFEKRVSDYQKAGVMSKSTKQEAGAFTFNEDF 419
>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 = 71.4 bits (175), Expect = 7e-17
Identities = 23/53 (43%), Positives = 36/53 (67%), Gaps = 2/53 (3%)
Query: 23 QHYFAENPFDFMENISLEGKTNFFERKVGEYQKSSVMAD--QDNQVFRLDEQF 73
++Y A NPF+FME+++ GKT FFE+KV +YQK+S M+ ++ D+ F
Sbjct: 293 KYYNAVNPFEFMEDVATAGKTTFFEKKVSDYQKASDMSKSATPSKEINFDDDF 345
>1syy_A Ribonucleoside-diphosphate reductase beta chain; DIIRON, oxygen
activation, iron coupled radical, immune EVAS
replication, oxidoreductase; 1.70A {Chlamydia
trachomatis} SCOP: a.25.1.2 PDB: 4d8g_A 4d8f_A 2ani_A
Length = 346
Score = 66.2 bits (162), Expect = 5e-15
Identities = 16/37 (43%), Positives = 23/37 (62%), Gaps = 1/37 (2%)
Query: 24 HYFAENPFDFM-ENISLEGKTNFFERKVGEYQKSSVM 59
Y +NPF +M E I L + NFFE +V EYQ ++ +
Sbjct: 308 IYHTKNPFPWMSETIDLNKEKNFFETRVIEYQHAASL 344
>4dr0_A Ribonucleoside-diphosphate reductase subunit beta; ribonucleotide
reductase, manganese, oxidoreductase; 1.90A {Bacillus
subtilis}
Length = 350
Score = 62.0 bits (151), Expect = 2e-13
Identities = 11/43 (25%), Positives = 19/43 (44%)
Query: 29 NPFDFMENISLEGKTNFFERKVGEYQKSSVMADQDNQVFRLDE 71
NP + +FF K Y+K++V +D+ + DE
Sbjct: 304 NPIVLNGLNTKTKSHDFFSMKGNGYKKATVEPLKDDDFYFEDE 346
>4a58_A Ribonucleoside-diphosphate reductase small chain; oxidoreductase,
epstein-BARR virus, R2 subunit; 1.68A {Human herpesvirus
4} PDB: 4a5c_A 4a5d_A 4a5e_A 4a5f_A 4a5h_A 4a5i_A 4a5j_A
Length = 324
Score = 58.8 bits (143), Expect = 2e-12
Identities = 10/36 (27%), Positives = 17/36 (47%), Gaps = 1/36 (2%)
Query: 24 HYFAENPFDF-MENISLEGKTNFFERKVGEYQKSSV 58
Y P D + ++ +TNFFE++ +Y V
Sbjct: 286 LYGTPPPKDCPLTYMTSIKQTNFFEQESSDYTMLVV 321
>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 = 50.4 bits (121), Expect = 2e-09
Identities = 6/36 (16%), Positives = 12/36 (33%), Gaps = 1/36 (2%)
Query: 29 NPFDFM-ENISLEGKTNFFERKVGEYQKSSVMADQD 63
NP + + + +FF Y + +D
Sbjct: 279 NPAILAALSPNADENHDFFSGSGSSYVMGKAVETED 314
>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 3uus_E* 1yfd_A 1piy_A 1r65_A
2xof_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 ...
Length = 375
Score = 49.7 bits (119), Expect = 3e-09
Identities = 7/43 (16%), Positives = 14/43 (32%), Gaps = 2/43 (4%)
Query: 27 AENPFDFMENI--SLEGKTNFFERKVGEYQKSSVMADQDNQVF 67
NP ++ S + E +V Y + ++ D
Sbjct: 328 RSNPIPWINTWLVSDNVQVAPQEVEVSSYLVGQIDSEVDTDDL 370
>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 = 46.5 bits (111), Expect = 6e-08
Identities = 12/39 (30%), Positives = 18/39 (46%), Gaps = 2/39 (5%)
Query: 27 AENPFDFMENIS--LEGKTNFFERKVGEYQKSSVMADQD 63
NP ++ GK++FFE+K +Y K S D
Sbjct: 306 KHNPMKWIRAYEDVNSGKSDFFEQKSRQYAKVSADNGFD 344
>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
Length = 329
Score = 44.6 bits (106), Expect = 2e-07
Identities = 5/36 (13%), Positives = 10/36 (27%), Gaps = 1/36 (2%)
Query: 29 NPFDFM-ENISLEGKTNFFERKVGEYQKSSVMADQD 63
+P + + + +FF Y D
Sbjct: 289 SPAILSSLSPNADENHDFFSGSGSSYVIGKAEDTTD 324
>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 = 27.5 bits (61), Expect = 0.29
Identities = 5/12 (41%), Positives = 10/12 (83%)
Query: 24 HYFAENPFDFME 35
+ A+NPF++M+
Sbjct: 299 IFHAKNPFNWMD 310
>3olj_A Ribonucleoside-diphosphate reductase subunit M2; metal-binding,
HRRM2, oxidoreductase; 2.10A {Homo sapiens}
Length = 286
Score = 25.6 bits (56), Expect = 1.4
Identities = 7/11 (63%), Positives = 8/11 (72%)
Query: 24 HYFAENPFDFM 34
+ ENPFDFM
Sbjct: 276 VFRVENPFDFM 286
>3qir_A PIWI-like protein 2; structural genomics consortium, SGC, PAZ
domain, RNAI, RNA B RNA binding protein; 2.45A {Homo
sapiens} PDB: 3o7x_A
Length = 148
Score = 24.6 bits (53), Expect = 3.1
Identities = 9/40 (22%), Positives = 19/40 (47%)
Query: 32 DFMENISLEGKTNFFERKVGEYQKSSVMADQDNQVFRLDE 71
D M I + K +F + + V+ +N+ +R+D+
Sbjct: 7 DVMHAIYQQNKEHFQDECTKLLVGNIVITRYNNRTYRIDD 46
>1wrj_A Methylated-DNA--protein-cysteine methyltransferase; 2.00A
{Sulfolobus tokodaii}
Length = 156
Score = 24.1 bits (53), Expect = 4.5
Identities = 7/29 (24%), Positives = 10/29 (34%), Gaps = 1/29 (3%)
Query: 22 LQHYFAENPFDFMENISLEGKTNFFERKV 50
L YF D E + + F +V
Sbjct: 49 LDLYFEGKKVDLTEPVDFKPFNE-FRIRV 76
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.323 0.137 0.402
Gapped
Lambda K H
0.267 0.0713 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,052,655
Number of extensions: 45126
Number of successful extensions: 55
Number of sequences better than 10.0: 1
Number of HSP's gapped: 51
Number of HSP's successfully gapped: 15
Length of query: 73
Length of database: 6,701,793
Length adjustment: 43
Effective length of query: 30
Effective length of database: 5,501,190
Effective search space: 165035700
Effective search space used: 165035700
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 51 (23.5 bits)