RPS-BLAST 2.2.22 [Sep-27-2009]
Database: pdb70
24,244 sequences; 5,693,230 total letters
Searching..................................................done
Query= 537021.9.peg.75_1
(136 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 = 137 bits (347), Expect = 5e-34
Identities = 80/135 (59%), Positives = 100/135 (74%), Gaps = 1/135 (0%)
Query: 1 MVGIAEQYQYIMRDESLHLNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEATLLEIAYA 60
M+GI EQYQYI+RDE++HLNFGID+IN IK ENP +WT E QQ+ ++ A LEI YA
Sbjct: 213 MIGIGEQYQYILRDETIHLNFGIDLINGIKEENPEIWTPELQQEIVELIKRAVDLEIEYA 272
Query: 61 HETMPKGFVGLNAPSCEQYMQFIANRRCHQIGLEPLFKYTENPFPWMSEVIDLKKEKNFF 120
+ +P+G +GL A Y+Q IA+RR +IGL+P++ T+NPFPWMSE IDL KEKNFF
Sbjct: 273 QDCLPRGILGLRASMFIDYVQHIADRRLERIGLKPIYH-TKNPFPWMSETIDLNKEKNFF 331
Query: 121 ETRVTEYQQGAGLKW 135
ETRV EYQ A L W
Sbjct: 332 ETRVIEYQHAASLTW 346
>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 = 123 bits (310), Expect = 1e-29
Identities = 25/134 (18%), Positives = 57/134 (42%), Gaps = 6/134 (4%)
Query: 1 MVGIAEQYQYIMRDESLHLNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEATLLEIAYA 60
+ A+ + I+RDES+H + Q + +E++ + ++++ EI Y
Sbjct: 188 LTNTADIIRLIIRDESVHGYYIGYKYQQGVKKLSEAEQEEYKAYTFDLMYDLYENEIEYT 247
Query: 61 HETMPKGFVGLNAPSCEQYMQFIANRRCHQIGLEPLF---KYTENPFPWMSEVIDLKKEK 117
+ +G ++++++ AN+ + +G E LF + +P S + +
Sbjct: 248 EDIYDD--LGWTE-DVKRFLRYNANKALNNLGYEGLFPTDETKVSPAILSSLSPNADENH 304
Query: 118 NFFETRVTEYQQGA 131
+FF + Y G
Sbjct: 305 DFFSGSGSSYVIGK 318
>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 = 123 bits (310), Expect = 1e-29
Identities = 43/136 (31%), Positives = 70/136 (51%), Gaps = 9/136 (6%)
Query: 1 MVGIAEQYQYIMRDESLHLNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEATLLEIAYA 60
M G+ + I RDE LH +F + HL K +Q+ R ++ A +E +
Sbjct: 253 MPGLTFSNELISRDEGLHCDFACLMFK-------HLVHKPAEQRVREIITNAVRIEQEFL 305
Query: 61 HETMPKGFVGLNAPSCEQYMQFIANRRCHQIGLEPLFKYTENPFPWMSEVIDLKKEKNFF 120
E +P +G+N +QY++F+A+R ++G +F+ ENPF +M I L+ + NFF
Sbjct: 306 TEALPVKLIGMNCTLMKQYIEFVADRLMLELGFNKIFR-VENPFDFMEN-ISLEGKTNFF 363
Query: 121 ETRVTEYQQGAGLKWD 136
E RV EYQ+ +
Sbjct: 364 EKRVGEYQRMGVMSNS 379
>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 = 119 bits (298), Expect = 3e-28
Identities = 41/131 (31%), Positives = 67/131 (51%), Gaps = 9/131 (6%)
Query: 1 MVGIAEQYQYIMRDESLHLNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEATLLEIAYA 60
M G+ + I RDE LH +F + +K + ++ ++ EA +E Y
Sbjct: 279 MPGLTFSNELICRDEGLHTDFACLLFAHLKNKPDPAIVEK-------IVTEAVEIEQRYF 331
Query: 61 HETMPKGFVGLNAPSCEQYMQFIANRRCHQIGLEPLFKYTENPFPWMSEVIDLKKEKNFF 120
+ +P +G+NA QY++F+A+R G + +K ENPF +M E I L + NFF
Sbjct: 332 LDALPVALLGMNADLMNQYVEFVADRLLVAFGNKKYYK-VENPFDFM-ENISLAGKTNFF 389
Query: 121 ETRVTEYQQGA 131
E RV++YQ+
Sbjct: 390 EKRVSDYQKAG 400
>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 = 119 bits (298), Expect = 3e-28
Identities = 35/137 (25%), Positives = 60/137 (43%), Gaps = 6/137 (4%)
Query: 1 MVGIAEQYQYIMRDESLHLNFGIDVINQIK----IENPHLWTKEFQQKSRTMLHEATLLE 56
M G A+ + I RDE+LHL ++N ++ +E +Q+ + +A E
Sbjct: 224 MEGNAKIIRLIARDEALHLTGTQHMLNLLRSGADDPEMAEIAEECKQECYDLFVQAAQQE 283
Query: 57 IAYAHETM-PKGFVGLNAPSCEQYMQFIANRRCHQIGLEPLFKYTENPFPWMSEVIDLKK 115
+A +GLN QY+++I N R +GL+ F+ NP PW++ +
Sbjct: 284 KDWADYLFRDGSMIGLNKDILCQYVEYITNIRMQAVGLDLPFQTRSNPIPWINTWLVSDN 343
Query: 116 EK-NFFETRVTEYQQGA 131
+ E V+ Y G
Sbjct: 344 VQVAPQEVEVSSYLVGQ 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 = 118 bits (296), Expect = 5e-28
Identities = 26/139 (18%), Positives = 55/139 (39%), Gaps = 6/139 (4%)
Query: 1 MVGIAEQYQYIMRDESLHLNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEATLLEIAYA 60
+ A+ + I+RDE++H + + + +E + + +L E E+ Y
Sbjct: 178 LTNTADLIRLIIRDEAVHGYYIGYKYQKNMEKISLGQREELKSFAFDLLLELYDNELQYT 237
Query: 61 HETMPKGFVGLNAPSCEQYMQFIANRRCHQIGLEPLF---KYTENPFPWMSEVIDLKKEK 117
E + A + ++ + AN+ +G EPLF NP + + +
Sbjct: 238 DELYAET---PWADDVKAFLCYNANKALMNLGYEPLFPAEMAEVNPAILAALSPNADENH 294
Query: 118 NFFETRVTEYQQGAGLKWD 136
+FF + Y G ++ +
Sbjct: 295 DFFSGSGSSYVMGKAVETE 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 = 112 bits (282), Expect = 2e-26
Identities = 35/134 (26%), Positives = 61/134 (45%), Gaps = 9/134 (6%)
Query: 1 MVGIAEQYQYIMRDESLHLNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEATLLEIAYA 60
M G+A + I RD + +F + HL TK + ++ EA +E Y
Sbjct: 206 MPGLAMANRNICRDRGAYTDFSCLLFA-------HLRTKPNPKIIEKIITEAVEIEKEYY 258
Query: 61 HETMPKGFVGLNAPSCEQYMQFIANRRCHQIGLEPLFKYTENPFPWMSEVIDLKKEKNFF 120
++P G++ S Y++F+A+ G E + NPF +M +V K FF
Sbjct: 259 SNSLPVEKFGMDLKSIHTYIEFVADGLLQGFGNEKYYN-AVNPFEFMEDVATAGK-TTFF 316
Query: 121 ETRVTEYQQGAGLK 134
E +V++YQ+ + +
Sbjct: 317 EKKVSDYQKASDMS 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 = 112 bits (281), Expect = 3e-26
Identities = 24/139 (17%), Positives = 52/139 (37%), Gaps = 6/139 (4%)
Query: 1 MVGIAEQYQYIMRDESLHLNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEATLLEIAYA 60
+ A+ + I+RDE++H + + + +E + + +L E EI Y
Sbjct: 178 LTNTADLIRLIIRDEAVHGYYIGYKYQIALQKLSAIEREELKLFALDLLMELYDNEIRYT 237
Query: 61 HETMPKGFVGLNAPSCEQYMQFIANRRCHQIGLEPLF---KYTENPFPWMSEVIDLKKEK 117
+ + ++ + AN+ +G E LF NP + + +
Sbjct: 238 EALYAET---GWVNDVKAFLCYNANKALMNLGYEALFPPEMADVNPAILAALSPNADENH 294
Query: 118 NFFETRVTEYQQGAGLKWD 136
+FF + Y G ++ +
Sbjct: 295 DFFSGSGSSYVMGKTVETE 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 = 101 bits (253), Expect = 4e-23
Identities = 38/131 (29%), Positives = 71/131 (54%), Gaps = 9/131 (6%)
Query: 1 MVGIAEQYQYIMRDESLHLNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEATLLEIAYA 60
+ G+ + I RDE LH +F + + ++ + P + + EA +E ++
Sbjct: 212 LHGLTFSNELISRDEGLHTDFNCLIYSLLENKLPENVVQNIVK-------EAVEVERSFI 264
Query: 61 HETMPKGFVGLNAPSCEQYMQFIANRRCHQIGLEPLFKYTENPFPWMSEVIDLKKEKNFF 120
E++P +G+N+ QY++F+A+R +G +F ++NPF WM ++I L+ + NFF
Sbjct: 265 CESLPCDLIGMNSRLMSQYIEFVADRLLECLGCSKVFH-SKNPFNWM-DLISLQGKTNFF 322
Query: 121 ETRVTEYQQGA 131
E RV +YQ+
Sbjct: 323 EKRVADYQKSG 333
>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 = 96.4 bits (239), Expect = 2e-21
Identities = 40/133 (30%), Positives = 67/133 (50%), Gaps = 2/133 (1%)
Query: 1 MVGIAEQYQYIMRDESLHLNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEATLLEIAYA 60
MV + YI RDE LH+ ++ ++ +E P L T+E + +T L +A LE +
Sbjct: 206 MVSTSTMINYINRDEQLHVYLFTNIFKELLVEFPELNTEETKTFVKTTLMKAADLEKDWF 265
Query: 61 HETMPKGFVGLNAPSCEQYMQFIANRRCHQIGLEPLF-KYTENPFPWMSEVIDLKKEK-N 118
+ G+N E Y+ FIAN+R Q+G+E + + NP W+ D+ K +
Sbjct: 266 RYIIGDKIPGINPEDMETYISFIANKRAVQLGMEKPYPEIKHNPMKWIRAYEDVNSGKSD 325
Query: 119 FFETRVTEYQQGA 131
FFE + +Y + +
Sbjct: 326 FFEQKSRQYAKVS 338
>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 = 87.4 bits (216), Expect = 9e-19
Identities = 21/108 (19%), Positives = 48/108 (44%), Gaps = 4/108 (3%)
Query: 1 MVGIAEQYQYIMRDESLHLNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEATLLEIAYA 60
+ A+ + I+RDES+H + Q + +E++ + ++++ EI Y
Sbjct: 187 LTNTADIIRLIIRDESVHGYYIGYKYQQGVKKLSEAEQEEYKAYTFDLMYDLYENEIEYT 246
Query: 61 HETMPKGFVGLNAPSCEQYMQFIANRRCHQIGLEPLFKYTENPF-PWM 107
+ +G ++++++ AN+ + +G E LF E P +
Sbjct: 247 EDIYDD--LGWTE-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 = 85.6 bits (211), Expect = 3e-18
Identities = 28/107 (26%), Positives = 55/107 (51%), Gaps = 8/107 (7%)
Query: 1 MVGIAEQYQYIMRDESLHLNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEATLLEIAYA 60
+ G+ + I RDE LH +F + + ++ + P + ++ EA +E ++
Sbjct: 211 LHGLTFSNELISRDEGLHTDFNCLIYSLLENKLPEEVVQN-------IVKEAVEVERSFI 263
Query: 61 HETMPKGFVGLNAPSCEQYMQFIANRRCHQIGLEPLFKYTENPFPWM 107
E++P +G+N+ QY++F+A+R +G +F +NPF WM
Sbjct: 264 CESLPCDLIGMNSRLMSQYIEFVADRLLECLGSPKIFH-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 = 84.8 bits (209), Expect = 6e-18
Identities = 17/123 (13%), Positives = 42/123 (34%), Gaps = 7/123 (5%)
Query: 1 MVGIAEQYQYIMRDESLHLNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEATLLEIAYA 60
+ G+ E + I DE H+ +G + + W F+ + ++ A L
Sbjct: 197 LPGMQELVRRIGDDERRHMAWGTFTCRRHVAADDANW-TVFETRMNELIPLALRLIEEGF 255
Query: 61 HETMPKGFVGLNAPSCEQYMQFIANRRCHQIGLEPLFKYTENPFPWMS-EVIDLKKEKNF 119
+ L+ + ++Q+ ++ + G + P + + + E F
Sbjct: 256 ALYGDQPPFDLSK---DDFLQYSTDKGMRRFGTISNAR--GRPVAEIDVDYSPAQLEDTF 310
Query: 120 FET 122
+
Sbjct: 311 ADE 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 = 29.5 bits (66), Expect = 0.26
Identities = 15/105 (14%), Positives = 27/105 (25%), Gaps = 48/105 (45%)
Query: 4 IAEQYQYIMRDESL---HLNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEATLLEIAYA 60
AE ++R G++++ W L
Sbjct: 191 SAETLSELIRTTLDAEKVFTQGLNILE---------W-----------LENP-------- 222
Query: 61 HETMP-KGFVGLNAP-SCE--------QYMQFIANRRCHQIGLEP 95
P K ++ L+ P SC Y+ + +G P
Sbjct: 223 -SNTPDKDYL-LSIPISCPLIGVIQLAHYV--VT---AKLLGFTP 260
Score = 29.1 bits (65), Expect = 0.37
Identities = 20/144 (13%), Positives = 44/144 (30%), Gaps = 49/144 (34%)
Query: 12 MRDESLH---LNFGIDVINQIKIENP-HLWTKEFQQKSRTMLHEATLLEIAYAHETMPKG 67
R +L L + V P + Q + + L E +G
Sbjct: 6 TRPLTLSHGSLEHVLLV--------PTASFFIASQLQEQ---FNKILPEPT-------EG 47
Query: 68 FVGLNAPS-----CEQYMQFIANRRC-HQIG-----LEPLFKYTENPFPWMSEV------ 110
F + P+ +++ ++++ ++G L EN + +++
Sbjct: 48 FAADDEPTTPAELVGKFLGYVSSLVEPSKVGQFDQVLNLCLTEFENCYLEGNDIHALAAK 107
Query: 111 --------IDLKKE--KNFFETRV 124
+ KE KN+ R+
Sbjct: 108 LLQENDTTLVKTKELIKNYITARI 131
>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 = 27.1 bits (59), Expect = 1.3
Identities = 27/96 (28%), Positives = 34/96 (35%), Gaps = 34/96 (35%)
Query: 7 QYQYIMRDESLHLNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEA----------TLLE 56
Q +M D LN G+ + P L KEF K R L E T LE
Sbjct: 719 QKSPVMAD----LNGGLQFV-------PEL--KEFTAKLRKELVETSEVRKAVSIETALE 765
Query: 57 ----------IAYAH-ETMPKGFVGLNAPSCEQYMQ 81
AYA E P+ + L+ P + Y Q
Sbjct: 766 HKVVNGNSADAAYAQVEIQPRANIQLDFPELKPYKQ 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 = 26.1 bits (56), Expect = 3.0
Identities = 7/25 (28%), Positives = 14/25 (56%), Gaps = 6/25 (24%)
Query: 42 QQKSRTMLHEATL-LEIAYAHETMP 65
+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 = 24.9 bits (54), Expect = 6.0
Identities = 12/34 (35%), Positives = 13/34 (38%), Gaps = 1/34 (2%)
Query: 22 GIDVINQIKIENPHLWTKEFQQKSRTMLHEATLL 55
+ KIEN L K F K M E LL
Sbjct: 30 NFKIEKIKKIENSELLDK-FTWKKSQMKEEGKLL 62
>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 = 24.8 bits (54), Expect = 6.0
Identities = 6/12 (50%), Positives = 10/12 (83%)
Query: 11 IMRDESLHLNFG 22
+++DE HLN+G
Sbjct: 154 VVKDEYTHLNYG 165
>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 = 7.4
Identities = 12/48 (25%), Positives = 25/48 (52%)
Query: 19 LNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEATLLEIAYAHETMPK 66
+NFG+ + + E H W +E ++SR ++ + T +I + +T
Sbjct: 117 MNFGLYPMLERFKEFAHGWEREHLERSRDLVFKNTFADIEFILKTCGG 164
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 0.136 0.422
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: 1,191,654
Number of extensions: 49721
Number of successful extensions: 152
Number of sequences better than 10.0: 1
Number of HSP's gapped: 126
Number of HSP's successfully gapped: 31
Length of query: 136
Length of database: 5,693,230
Length adjustment: 83
Effective length of query: 53
Effective length of database: 3,680,978
Effective search space: 195091834
Effective search space used: 195091834
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: 51 (24.0 bits)