RPS-BLAST 2.2.22 [Sep-27-2009]
Database: mmdb70
33,805 sequences; 4,956,049 total letters
Searching..................................................done
Query= gi|254781006|ref|YP_003065419.1| ribonucleotide-diphosphate
reductase subunit beta [Candidatus Liberibacter asiaticus str. psy62]
(125 letters)
>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:150-346)
Length = 197
Score = 118 bits (296), Expect = 3e-28
Identities = 38/128 (29%), Positives = 63/128 (49%), Gaps = 3/128 (2%)
Query: 1 MRDESLHLNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEATLLEIAYAHETMPKGFVGL 60
RDE LH+ ++ ++ +E P L T+E + +T L +A LE + + G+
Sbjct: 68 NRDEQLHVYLFTNIFKELLVEFPELNTEETKTFVKTTLXKAADLEKDWFRYIIGDKIPGI 127
Query: 61 NAPSCEQYMQFIANRRCHQIGLEPLFK-YTENPFPWMSEVIDLKKEK-NFFETRVTEYQQ 118
N E Y+ FIAN+R Q+G E + NP W+ D+ K +FFE + +Y +
Sbjct: 128 NPEDXETYISFIANKRAVQLGXEKPYPEIKHNPXKWIRAYEDVNSGKSDFFEQKSRQYAK 187
Query: 119 G-AELKWD 125
A+ +D
Sbjct: 188 VSADNGFD 195
>1r2f_A Protein (ribonucleotide reductase R2); nucleotide
metabolism, oxidoreductase; 2.10A {Salmonella
typhimurium} (A:129-319)
Length = 191
Score = 114 bits (286), Expect = 5e-27
Identities = 23/129 (17%), Positives = 45/129 (34%), Gaps = 7/129 (5%)
Query: 1 MRDESLHLNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEATLLEIAYAHETMPKGFVGL 60
+RDE++H + + + +E + + +L E EI Y
Sbjct: 61 IRDEAVHGYYIGYKYQIALQKLSAIEREELKLFALDLLMELYDNEIRYTEALYA---ETG 117
Query: 61 NAPSCEQYMQFIANRRCHQIGLEPLFKYTE---NPFPWMSEVIDLKKEKNFFETRVTEYQ 117
+ ++ + AN+ +G E LF NP + + + +FF + Y
Sbjct: 118 WVNDVKAFLCYNANKALMNLGYEALFPPEMADVNPAILAALSPNADENHDFFSGSGSSYV 177
Query: 118 QGAEL-KWD 125
G + D
Sbjct: 178 MGKTVETED 186
>1syy_A Ribonucleoside-diphosphate reductase beta chain; DIIRON,
oxygen activation, iron coupled radical, immune evasion,
replication; 1.70A {Chlamydia trachomatis} (A:)
Length = 346
Score = 111 bits (277), Expect = 4e-26
Identities = 71/124 (57%), Positives = 91/124 (73%), 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 RASMFIDYVQHIADRRLERIGLKPIY-HTKNPFPWMSETIDLNKEKNFFETRVIEYQHAA 342
Query: 121 ELKW 124
L W
Sbjct: 343 SLTW 346
>3dhz_A Ribonucleotide reductase subunit R2F; metal free, hydrogen
bond, metal binding protein; 1.63A {Corynebacterium
ammoniagenes} (A:139-329)
Length = 191
Score = 110 bits (277), Expect = 5e-26
Identities = 25/129 (19%), Positives = 53/129 (41%), Gaps = 7/129 (5%)
Query: 1 MRDESLHLNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEATLLEIAYAHETMPKGFVGL 60
+RDES+H + Q + +E++ + ++++ EI Y +
Sbjct: 61 IRDESVHGYYIGYKYQQGVKKLSEAEQEEYKAYTFDLMYDLYENEIEYTEDIYDDLG--- 117
Query: 61 NAPSCEQYMQFIANRRCHQIGLEPLF---KYTENPFPWMSEVIDLKKEKNFFETRVTEYQ 117
++++++ AN+ + +G E LF + +P S + + +FF + Y
Sbjct: 118 WTEDVKRFLRYNANKALNNLGYEGLFPTDETKVSPAILSSLSPNADENHDFFSGSGSSYV 177
Query: 118 QG-AELKWD 125
G AE D
Sbjct: 178 IGKAEDTTD 186
>1jk0_B RNR Y4, ribonucleoside-diphosphate reductase small chain 2;
ribonucleotide reductase, oxidoreductase; 2.80A
{Saccharomyces cerevisiae} (B:147-345)
Length = 199
Score = 104 bits (261), Expect = 4e-24
Identities = 27/125 (21%), Positives = 56/125 (44%), Gaps = 9/125 (7%)
Query: 1 MRDESLHLNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEATLLEIAYAHETMPKGFVGL 60
RD + +F + ++ + ++ ++ EA +E Y ++P G+
Sbjct: 71 CRDRGAYTDFSCLLFAHLRTKPNPKIIEK-------IITEAVEIEKEYYSNSLPVEKFGM 123
Query: 61 NAPSCEQYMQFIANRRCHQIGLEPLFKYTENPFPWMSEVIDLKKEKNFFETRVTEYQQGA 120
+ S Y++F+A+ G E + NPF +M +V K FFE +V++YQ+ +
Sbjct: 124 DLKSIHTYIEFVADGLLQGFGNEKYYN-AVNPFEFMEDVATAGK-TTFFEKKVSDYQKAS 181
Query: 121 ELKWD 125
++
Sbjct: 182 DMSKS 186
>1jk0_A RNR Y2, ribonucleoside-diphosphate reductase small chain 1;
ribonucleotide reductase, oxidoreductase; 2.80A
{Saccharomyces cerevisiae} (A:1-103,A:228-419)
Length = 295
Score = 103 bits (259), Expect = 7e-24
Identities = 35/124 (28%), Positives = 60/124 (48%), Gaps = 9/124 (7%)
Query: 1 MRDESLHLNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEATLLEIAYAHETMPKGFVGL 60
RDE LH +F + +K + ++ ++ EA +E Y + +P +G+
Sbjct: 166 CRDEGLHTDFACLLFAHLKNKPDPAIVEK-------IVTEAVEIEQRYFLDALPVALLGM 218
Query: 61 NAPSCEQYMQFIANRRCHQIGLEPLFKYTENPFPWMSEVIDLKKEKNFFETRVTEYQQGA 120
NA QY++F+A+R G + + ENPF +M + K NFFE RV++YQ+
Sbjct: 219 NADLMNQYVEFVADRLLVAFGNKKYY-KVENPFDFMENISLAGK-TNFFEKRVSDYQKAG 276
Query: 121 ELKW 124
+
Sbjct: 277 VMSK 280
>1h0o_A Ribonucleoside-diphosphate reductase; oxidoreductase,
ribonucleotide reductase, dinuclear metal-cluster; 2.2A
{Mus musculus} (A:219-390)
Length = 172
Score = 101 bits (252), Expect = 5e-23
Identities = 36/125 (28%), Positives = 60/125 (48%), Gaps = 9/125 (7%)
Query: 1 MRDESLHLNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEATLLEIAYAHETMPKGFVGL 60
RDE LH +F + + + +E ++ A +E + E +P +G+
Sbjct: 46 SRDEGLHCDFACLMFKHLVHKPAEQRVRE-------IITNAVRIEQEFLTEALPVKLIGM 98
Query: 61 NAPSCEQYMQFIANRRCHQIGLEPLFKYTENPFPWMSEVIDLKKEKNFFETRVTEYQQGA 120
N +QY++F+A+R ++G ENPF +M E I L+ + NFFE RV EYQ+
Sbjct: 99 NCTLMKQYIEFVADRLMLELGFNK-IFRVENPFDFM-ENISLEGKTNFFEKRVGEYQRMG 156
Query: 121 ELKWD 125
+
Sbjct: 157 VMSNS 161
>1mxr_A Ribonucleotide reductase R2; radical protein, DI iron,
oxidoreductase; 1.42A {Escherichia coli} (A:)
Length = 375
Score = 99.5 bits (247), Expect = 1e-22
Identities = 32/126 (25%), Positives = 55/126 (43%), Gaps = 6/126 (4%)
Query: 1 MRDESLHLNFGIDVINQIKIENPHLWT----KEFQQKSRTMLHEATLLEIAYAHETMPKG 56
RDE+LHL ++N ++ +E +Q+ + +A E +A G
Sbjct: 235 ARDEALHLTGTQHMLNLLRSGADDPEMAEIAEECKQECYDLFVQAAQQEKDWADYLFRDG 294
Query: 57 -FVGLNAPSCEQYMQFIANRRCHQIGLEPLFKYTENPFPWMSEVIDLKKEK-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
>2p1i_A Ribonucleotide reductase, small chain; F222 twinning,
plasmodb PY03671, structural genomics consortium, SGC,
oxidoreductase; 2.70A {Plasmodium yoelii yoelii str}
(A:162-349)
Length = 188
Score = 98.9 bits (246), Expect = 2e-22
Identities = 36/125 (28%), Positives = 68/125 (54%), Gaps = 9/125 (7%)
Query: 1 MRDESLHLNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEATLLEIAYAHETMPKGFVGL 60
RDE LH +F + + ++ + P + ++ EA +E ++ E++P +G+
Sbjct: 62 SRDEGLHTDFNCLIYSLLENKLPENVVQN-------IVKEAVEVERSFICESLPCDLIGM 114
Query: 61 NAPSCEQYMQFIANRRCHQIGLEPLFKYTENPFPWMSEVIDLKKEKNFFETRVTEYQQGA 120
N+ QY++F+A+R +G +F ++NPF WM ++I L+ + NFFE RV +YQ+
Sbjct: 115 NSRLMSQYIEFVADRLLECLGCSKVFH-SKNPFNWM-DLISLQGKTNFFEKRVADYQKSG 172
Query: 121 ELKWD 125
+
Sbjct: 173 VMAQR 177
>2o1z_A Ribonucleotide reductase subunit R2; small subunit
ribonucleotide reductase, oxidoreductase, DNA
replication, iron, DIIRON, radical, R2 subunit; 2.40A
{Plasmodium vivax} (A:161-311)
Length = 151
Score = 86.5 bits (214), Expect = 1e-18
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: 62 SRDEGLHTDFNCLIYSLLENKLPEEVVQN-------IVKEAVEVERSFICESLPCDLIGM 114
Query: 61 NAPSCEQYMQFIANRRCHQIGLEPLFKYTENPFPWM 96
N+ QY++F+A+R +G +F +NPF WM
Sbjct: 115 NSRLMSQYIEFVADRLLECLGSPKIFH-AKNPFNWM 149
>3ee4_A Probable ribonucleoside-diphosphate reductase; manganese,
iron, DIIRON, carboxylate, oxidase, ligand, cavity,
monooxygenase; HET: MYR; 1.90A {Mycobacterium
tuberculosis} (A:)
Length = 323
Score = 81.8 bits (201), Expect = 3e-17
Identities = 16/120 (13%), Positives = 30/120 (25%), Gaps = 5/120 (4%)
Query: 1 MRDESLHLNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEATLLEIAYAHETMPKGFVGL 60
DE H+ +G + + W F+ + ++ A L + L
Sbjct: 208 GDDERRHMAWGTFTCRRHVAADDANW-TVFETRMNELIPLALRLIEEGFALYGDQPPFDL 266
Query: 61 NAPSCEQYMQFIANRRCHQIGLEPLFKYTENPFPWMSEVIDLKKEKNFFETRVTEYQQGA 120
+ QY RR I + + E F + +
Sbjct: 267 SKDDFLQYSTDKGMRRFGTISNARGR----PVAEIDVDYSPAQLEDTFADEDRRTLAAAS 322
>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 = 60.3 bits (145), Expect = 8e-11
Identities = 10/111 (9%), Positives = 31/111 (27%), Gaps = 11/111 (9%)
Query: 1 MRDESLHLNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEATLLEIAYAHETMPKGFVGL 60
+RDE+ H + ++V+ ++ + + L +++ + G+
Sbjct: 224 LRDETAHGSIVVEVVRELYARMNEQQRRALVRCLPIALEAFAEQDLSALLLELNA--AGI 281
Query: 61 NAPSC-EQYMQFIANRRCHQIGLEPLFKYTENPFPWMSEVIDLKKEKNFFE 110
++ A + + + L +F
Sbjct: 282 RGAEEIVGDLRSTAGGTRLVRDFSG-------ARKMVEQ-LGLDDAVDFDF 324
>3fho_A ATP-dependent RNA helicase DBP5; mRNA export, ATPase,
translation termination, ATP-binding, cytoplasm,
hydrolase, membrane; 2.80A {Schizosaccharomyces pombe}
(A:1-326)
Length = 326
Score = 26.3 bits (57), Expect = 1.5
Identities = 8/54 (14%), Positives = 17/54 (31%), Gaps = 9/54 (16%)
Query: 3 DESLHLNFGIDVINQIKIENPH-----L----WTKEFQQKSRTMLHEATLLEIA 47
D L D +IK P L +++ ++ + A + +
Sbjct: 269 DNMLDQQGLGDQSMRIKHLLPRNTQIVLFSATFSERVEKYAERFAPNANEIRLK 322
>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} (A:)
Length = 244
Score = 24.4 bits (53), Expect = 4.9
Identities = 12/41 (29%), Positives = 16/41 (39%), Gaps = 12/41 (29%)
Query: 1 MRDESLHLNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEA 41
++DE HLN+G W K + R L EA
Sbjct: 155 VKDEYTHLNYG------------EAWLKANLESCREELLEA 183
>3hn3_A Beta-G1, beta-glucuronidase; lysosomal enzyme, acid
hydrolase, glycosidase, alternative splicing, disease
mutation, glycoprotein, hydrolase; HET: NDG NAG BMA MAN
GUP; 1.70A {Homo sapiens} PDB: 1bhg_A* (A:206-306)
Length = 101
Score = 24.5 bits (53), Expect = 5.5
Identities = 3/21 (14%), Positives = 8/21 (38%)
Query: 9 NFGIDVINQIKIENPHLWTKE 29
G + + + P+L +
Sbjct: 51 TQGQLKVPGVSLWWPYLMHER 71
>2odr_A Phosphoseryl-tRNA synthetase; phosphoserine tRNA
synthetase class II, ligase; 3.23A {Methanococcus
maripaludis S2} (A:550-614)
Length = 65
Score = 24.3 bits (52), Expect = 5.6
Identities = 4/7 (57%), Positives = 6/7 (85%), Gaps = 1/7 (14%)
Query: 16 N-QIKIE 21
N ++KIE
Sbjct: 1 NVEVKIE 7
>2odr_B Phosphoseryl-tRNA synthetase; phosphoserine tRNA
synthetase class II, ligase; 3.23A {Methanococcus
maripaludis S2} (B:550-611)
Length = 62
Score = 23.9 bits (51), Expect = 7.2
Identities = 4/7 (57%), Positives = 6/7 (85%), Gaps = 1/7 (14%)
Query: 16 N-QIKIE 21
N ++KIE
Sbjct: 1 NVEVKIE 7
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 0.135 0.421
Gapped
Lambda K H
0.267 0.0714 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 33805
Number of Hits to DB: 952,230
Number of extensions: 37144
Number of successful extensions: 120
Number of sequences better than 10.0: 1
Number of HSP's gapped: 94
Number of HSP's successfully gapped: 24
Length of query: 125
Length of database: 4,956,049
Length adjustment: 75
Effective length of query: 50
Effective length of database: 2,420,674
Effective search space: 121033700
Effective search space used: 121033700
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: 50 (23.1 bits)