RPS-BLAST 2.2.22 [Sep-27-2009]
Database: mmdb70
33,805 sequences; 4,956,049 total letters
Searching..................................................done
Query= gi|254781120|ref|YP_003065533.1| radical SAM protein
[Candidatus Liberibacter asiaticus str. psy62]
(384 letters)
>2yx0_A Radical SAM enzyme; predicted tRNA modification enzyme,
metal binding protein, structural genomics, NPPSFA;
2.21A {Pyrococcus horikoshii} (A:)
Length = 342
Score = 115 bits (288), Expect = 9e-27
Identities = 44/346 (12%), Positives = 88/346 (25%), Gaps = 36/346 (10%)
Query: 38 IWKWIYV-RGIRDFQGMSDISQEVRHLLNQHFSIIYPEIVDEKISCDGTRKWLLRFP-AR 95
+ + I + G Q ++ +EV L + EIV K +
Sbjct: 1 MMEMITIKPGKITVQANPNMPKEVAELFRKQH----YEIVGR----HSGVKLCHWLKKSL 52
Query: 96 CIGGPVEIETVYIPEKSRGTLCVSSQVGCSLTCSFCY------TGTQKLVRNLTAEEILL 149
G + Y R C+ C FC+ GT+ I+
Sbjct: 53 TEGRFCYKQKFYGIHSHRCLQMTPVLAWCTHNCIFCWRPMENFLGTELPQPWDDPAFIVE 112
Query: 150 QVLLARSLLGDFPGCEDIEGMVIPSVGRKISNIVMMGMGEPLCNFDNVKKSLSIASDSMG 209
+ + A+ L ++ + GEP + + +
Sbjct: 113 ESIKAQRKLLIGYKGNPKVDKKKFEEAWNPTHAAISLSGEP-MLYPYMGDLVEEFHK--- 168
Query: 210 LSFSKRRITLSTSGFVPNIARVGEEIG---VMLAISLHAVSNDLRNILVPINRKYPLEML 266
+ T+G +P + L +S+ A + N + E +
Sbjct: 169 ---RGFTTFIVTNGTIPERLEEMIKEDKLPTQLYVSITAPDIETYNSVNIPMIPDGWERI 225
Query: 267 IDACRHYPGLSNARRITFEYVMLKGINDSPRDALNLIKILKGI-PAKINLIPFNPWPGCE 325
+ R ++KG N K++ P + +
Sbjct: 226 LRFLELM--RDLPTRTVVRLTLVKGENM--HSPEKYAKLILKARPMFVEAKAYMFVGYSR 281
Query: 326 Y-----LCSDQKDIVTFSECIKRSGYSSPIRTPRGLDILAACGQLK 366
+DI F+E + + I + +
Sbjct: 282 NRLTINNMPSHQDIREFAEALVKHLPGYHIEDEYEPSRVVLIMRDD 327
>2z2u_A UPF0026 protein MJ0257; metal binding protein; 2.40A
{Methanocaldococcus jannaschii} (A:)
Length = 311
Score = 94.4 bits (233), Expect = 2e-20
Identities = 39/329 (11%), Positives = 87/329 (26%), Gaps = 43/329 (13%)
Query: 56 ISQEVRHLLNQHFSIIYPEIVDEKISCDGTRKWLLRFPARCIGGPVEIETVYIPEKSRGT 115
I +E+ +L + I + W Y E R
Sbjct: 2 IPEEIYKILRKQRYQIDGH------TAVKLCGW--VRKKMLEDKNCYKSKFYGIETHRCI 53
Query: 116 LCVSSQVGCSLTCSFCYTGTQKLVRNLTAEEILLQVLLAR-----SLLGDFPGC------ 164
C S + C C FC+ + + ++ + L
Sbjct: 54 QCTPSVIWCQQNCIFCWRVLPRDIGIDISQIKEPKWEEPEVVYEKILAMHKRIIMGYAGV 113
Query: 165 EDIEGMVIPSVGRKISNIVMMGMGEPLCNFDNVKKSLSIASDSMGLSFSKRRITLSTSGF 224
D G + ++ + GEP + + + ++G
Sbjct: 114 LDRVGEKKFKEALEPKHVAISLSGEPTLYPYLDELIKIFHKNGF-------TTFVVSNGI 166
Query: 225 VPNIARVGEEIGVMLAISLHAVSNDLRNILVPINRKYPLEMLIDACRHYPGLSNARRITF 284
+ ++ + L ISL A D + +K E +++ +R
Sbjct: 167 LTDVIE--KIEPTQLYISLDAYDLDSYRRICG-GKKEYWESILNTLDIL---KEKKRTCI 220
Query: 285 EYVMLKGINDSPRDALNLIKILKGIPAKINLIPFNPWPGCEYLCSDQK-----DIVTFSE 339
+++G ND + L + I L + + + +I+ ++
Sbjct: 221 RTTLIRGYNDDILKFVELYERAD--VHFIELKSYMHVGYSQKRLKKEDMLQHDEILKLAK 278
Query: 340 CIKRSGYSSPIRTPRGLDILAACGQLKSL 368
+ + I + L++
Sbjct: 279 MLDENSSYKLIDD----SEDSRVALLQNE 303
>3c8f_A Pyruvate formate-lyase 1-activating enzyme; adoMet radical,
SAM radical, activase, glycyl radical, 4Fe- 4S,
carbohydrate metabolism, cytoplasm; HET: MT2 PGE; 2.25A
{Escherichia coli} PDB: 3cb8_A* (A:)
Length = 245
Score = 77.9 bits (190), Expect = 2e-15
Identities = 32/219 (14%), Positives = 71/219 (32%), Gaps = 32/219 (14%)
Query: 113 RGTLCVSSQVGCSLTCSFCY---TGTQKLVRNLTAEEILLQVLLARSLLGDFPGCEDIEG 169
G ++ GC + C +C+ T + +T E+++ +V+ R
Sbjct: 18 PGIRFITFFQGCLMRCLYCHNRDTWDTHGGKEVTVEDLMKEVVTYRHF------------ 65
Query: 170 MVIPSVGRKISNIVMMGMGEPLCNFDNVKKSLSIASDSMGLSFSKRRITLSTSGFVPNIA 229
V GE + + V+ T +
Sbjct: 66 ------MNASGGGVTASGGEAILQAEFVRDWFRACKKEG---IHTCLDTNGFVRRYDPVI 116
Query: 230 RVGEEIGVMLAISLHAVSNDLRNILVPINRKYPLEMLIDACRHYPGLSNARRITFEYVML 289
E+ ++ + L +++++ LV ++ LE ++ YV++
Sbjct: 117 DELLEVTDLVMLDLKQMNDEIHQNLVGVSNHRTLEFAKYLANKNV------KVWIRYVVV 170
Query: 290 KGINDSPRDALNLIKILK--GIPAKINLIPFNPWPGCEY 326
G +D A L + + G KI L+P++ ++
Sbjct: 171 PGWSDDDDSAHRLGEFTRDMGNVEKIELLPYHELGKHKW 209
>3can_A Pyruvate-formate lyase-activating enzyme; structural
genomics, PSI, MCSG, APC20359.1; 1.80A {Bacteroides
vulgatus atcc 8482} (A:)
Length = 182
Score = 74.9 bits (183), Expect = 1e-14
Identities = 17/151 (11%), Positives = 40/151 (26%), Gaps = 14/151 (9%)
Query: 177 RKISNIVMMGMGEPLCNFDNVKKSLSIASDSMGLSFSKRRITLSTSGFVPNIARVGEEIG 236
+ G GEPL + + + L + T+
Sbjct: 2 NAGGGVTFCG-GEPLLHPEFLIDILKRCGQ------QGIHRAVDTTLLARKETVDEVXRN 54
Query: 237 VML-AISLHAVSNDLRNILVPINRKYPLEMLIDACRHYPGLSNARRITFEYVMLKGINDS 295
L I L + + + + + L+ + +++G+N
Sbjct: 55 CELLLIDLKSXDSTVHQTFCDVPNELILKNIRRVAEAD------FPYYIRIPLIEGVNAD 108
Query: 296 PRDALNLIKILKGIPAKINLIPFNPWPGCEY 326
++ + L +P +I P+
Sbjct: 109 EKNIKLSAEFLASLPRHPEIINLLPYHDIGK 139
>2a5h_A L-lysine 2,3-aminomutase; radical SAM, four-iron-four-sulfur
cluster, 4Fe4S, FS4, SAM, S-adenosylmethionine,
alpha-beta channel; HET: SAM LYS PLP; 2.10A {Clostridium
subterminale} (A:95-342)
Length = 248
Score = 73.3 bits (178), Expect = 5e-14
Identities = 30/273 (10%), Positives = 75/273 (27%), Gaps = 38/273 (13%)
Query: 100 PVEIETVYIPEKSR-----GTLCVSSQVGCSLTCSFCYT-GTQKLVRNLTAEEILLQVLL 153
P+ E P + + CS C C + E + + +
Sbjct: 3 PLH-EDTDSPVPGLTHRYPDRVLLLITDXCSXYCRHCTRRRFAGQSDDSXPXERIDKAI- 60
Query: 154 ARSLLGDFPGCEDIEGMVIPSVGRKISNIVMMGMGEPLCNFDNVKKSLSIASDSMGLSFS 213
++ ++++ G L + + ++ ++ + +
Sbjct: 61 -----------------DYIRNTPQVRDVLLSGGDALLVSDETLEYIIAKLREIPHV--- 100
Query: 214 KRRITLSTSGFVPNIARVGEEIGVMLAISLHAVSNDLRNILVPINRKYPLEMLIDACRHY 273
+ + + V R+ ++ + + + E AC+
Sbjct: 101 -EIVRIGSRTPVVLPQRI-----TPELVNXLKKYHPVWLNTHFNHPNEITEESTRACQLL 154
Query: 274 PGLSNARRITFEYVMLKGINDSPRDALNLIKILKGIPA-KINLIPFNPWPGCEYLCSDQK 332
+ + V+L+G+ND L+ L I + + G E+ +
Sbjct: 155 --ADAGVPLGNQSVLLRGVNDCVHVXKELVNKLVKIRVRPYYIYQCDLSLGLEHFRTPVS 212
Query: 333 DIVTFSECIKRSGYSSPIRTPRGLDILAACGQL 365
+ E + R S +D G+
Sbjct: 213 KGIEIIEGL-RGHTSGYCVPTFVVDAPGGGGKT 244
>1tv8_A MOAA, molybdenum cofactor biosynthesis protein A; TIM
barrel, ligand binding protein; HET: SAM; 2.20A
{Staphylococcus aureus} (A:1-313)
Length = 313
Score = 38.0 bits (86), Expect = 0.002
Identities = 26/222 (11%), Positives = 61/222 (27%), Gaps = 24/222 (10%)
Query: 111 KSRGTLCVSSQVGCSLTCSFCYT-GTQKLVRNLTAEEILLQVLLARSLLGDFPGCEDIEG 169
+ L +S C+ C +C + LL +++
Sbjct: 11 RPIRDLRLSVTDRCNFRCDYCMPKEVFGDDFVFLPKNELLTF-------------DEMAR 57
Query: 170 MVIPSVGRKISNIVMMGMGEPLCNFDNVKKSLSIASDSMGLSFSKRRITLSTSGFVPNIA 229
+ + I + G GEPL D + I L+T+G +
Sbjct: 58 IAKVYAELGVKKIRITG-GEPLMRRDLDVLIAKLNQI-----DGIEDIGLTTNGLLLKKH 111
Query: 230 RVGEEIGVMLAISLHAVSNDLRNILVPINRKYPLEMLIDACRHYPGLSNARRITFEYVML 289
+ I++ + D NR +++ + + + + ++
Sbjct: 112 GQKLYDAGLRRINVSLDAIDDTLFQSINNRNIKATTILEQIDYA----TSIGLNVKVNVV 167
Query: 290 KGINDSPRDALNLIKILKGIPAKINLIPFNPWPGCEYLCSDQ 331
+ + +++ K +I I F +
Sbjct: 168 IQKGINDDQIIPMLEYFKDKHIEIRFIEFMDVGNDNGWDFSK 209
>1q74_A 1D-MYO-inosityl 2-acetamido-2-deoxy-alpha-D- glucopyranoside
deacetylase (MSHB); rossmann fold, zinc aminohydrolase;
HET: PE4; 1.70A {Mycobacterium tuberculosis} (A:)
Length = 303
Score = 27.6 bits (60), Expect = 2.9
Identities = 7/67 (10%), Positives = 16/67 (23%), Gaps = 6/67 (8%)
Query: 7 ESLIGMMREELEEALLKIGIPQRHV------RMRTSQIWKWIYVRGIRDFQGMSDISQEV 60
+ L G EL AL +G+ + + +
Sbjct: 62 DQLGGYRIGELTAALRALGVSAPIYLGGAGRWRDSGMAGTDQRSQRRFVDADPRQTVGAL 121
Query: 61 RHLLNQH 67
++ +
Sbjct: 122 VAIIREL 128
>3his_A Vacuolar saporin; transition state analogue, ribosome
inactivating proteins, RIPS, hydrolase, plant defense,
protein synthesis inhibitor; 1.49A {Saponaria
officinalis} PDB: 3hit_A* 3hiv_A* 3hiw_A* 3hiq_A
(A:1-194)
Length = 194
Score = 27.3 bits (60), Expect = 3.9
Identities = 7/38 (18%), Positives = 17/38 (44%)
Query: 8 SLIGMMREELEEALLKIGIPQRHVRMRTSQIWKWIYVR 45
+ + +R+++++ L G V R K++ V
Sbjct: 18 TFLKQLRDDIKDPNLHYGGTNLPVIKRPVGPPKFLRVN 55
>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} (A:1221-1330,A:1541-1688)
Length = 258
Score = 26.8 bits (59), Expect = 5.0
Identities = 7/46 (15%), Positives = 18/46 (39%), Gaps = 7/46 (15%)
Query: 21 LLKIGIPQRHVRMRTSQIWKWIYVRGIRDFQGMSDISQEVRHLLNQ 66
L + +R + R +QI W + + + + E + ++
Sbjct: 23 NLNMKYRKRQLVTREAQIKDW------VENE-LEALKLEAEEIPSE 61
>2get_A Pantothenate kinase; homodimer, COA biosynthesis,
nucleotide binding, transferase; HET: CME COK; 2.35A
{Mycobacterium tuberculosis H37RV} PDB: 2ges_A* 2geu_A*
2gev_A* 2zs7_A* 2zs8_A* 2zs9_A* 2zsa_A* 2zsb_A* 2zsd_A*
2zse_A* 2zsf_A* (A:1-131,A:196-312)
Length = 248
Score = 26.1 bits (57), Expect = 7.9
Identities = 7/67 (10%), Positives = 19/67 (28%), Gaps = 1/67 (1%)
Query: 1 MNFLKKESLIGMMREELEEALLKIGIPQRHVRMRTSQIWKWIYVRGIRDFQGMSDISQEV 60
M+ L + S + + L++ P + + + + + +
Sbjct: 1 MSRLSEPSPYVEF-DRRQWRALRMSTPLALTEEELVGLRGLGEQIDLLEVEEVYLPLARL 59
Query: 61 RHLLNQH 67
HL
Sbjct: 60 IHLQVAA 66
>3bij_A Uncharacterized protein GSU0716; alpha-beta protein,
structural genomics, PSI-2, protein structure
initiative; 2.50A {Geobacter sulfurreducens pca} (A:)
Length = 285
Score = 26.0 bits (56), Expect = 8.0
Identities = 5/38 (13%), Positives = 13/38 (34%)
Query: 246 VSNDLRNILVPINRKYPLEMLIDACRHYPGLSNARRIT 283
+ ++L +L + + D+C + A
Sbjct: 111 IDDELYALLGKFAAGVRVLVFSDSCHSGTVVKXAYYNG 148
>3bh1_A UPF0371 protein DIP2346; structural genomics, unknown
function, protein structure initiative, PSI-2; 2.51A
{Corynebacterium diphtheriae NCTC13129} (A:345-507)
Length = 163
Score = 26.2 bits (58), Expect = 8.3
Identities = 8/18 (44%), Positives = 11/18 (61%)
Query: 300 LNLIKILKGIPAKINLIP 317
LN +K L GI I+L+
Sbjct: 46 LNALKHLAGIDDAIHLLS 63
>1r30_A Biotin synthase; SAM radical protein, TIM barrel, FES
cluster, transferase; HET: SAM DTB; 3.40A {Escherichia
coli} (A:)
Length = 369
Score = 25.9 bits (55), Expect = 8.5
Identities = 8/70 (11%), Positives = 18/70 (25%), Gaps = 5/70 (7%)
Query: 123 GCSLTCSFCYTGT-----QKLVRNLTAEEILLQVLLARSLLGDFPGCEDIEGMVIPSVGR 177
C C +C + + R + E++L A++
Sbjct: 75 ACPEDCKYCPQSSRYKTGLEAERLMEVEQVLESARKAKAAGSTRFCMGAAWKNPHERDMP 134
Query: 178 KISNIVMMGM 187
+ +V
Sbjct: 135 YLEQMVQGVK 144
>2pif_A UPF0317 protein pspto_5379; UPF0317 family, structural
genomics, PSI-2, protein structure initiative; 2.30A
{Pseudomonas syringae PV} (A:126-234)
Length = 109
Score = 25.8 bits (57), Expect = 8.8
Identities = 6/15 (40%), Positives = 8/15 (53%)
Query: 17 LEEALLKIGIPQRHV 31
E L + GI RH+
Sbjct: 3 FETPLQEAGIEVRHI 17
>1umk_A B5R, NADH-cytochrome B5 reductase; flavoprotein, beta
barrel, FAD-binding domain, NADH-binding domain,
oxidoreductase; HET: FAD; 1.75A {Homo sapiens}
(A:147-275)
Length = 129
Score = 25.8 bits (56), Expect = 9.4
Identities = 4/21 (19%), Positives = 7/21 (33%)
Query: 11 GMMREELEEALLKIGIPQRHV 31
M++ L +G P
Sbjct: 106 PMIQYACLPNLDHVGHPTERC 126
>2abk_A Endonuclease III; DNA-repair, DNA glycosylase; 1.85A
{Escherichia coli} (A:23-133)
Length = 111
Score = 26.0 bits (57), Expect = 9.6
Identities = 13/34 (38%), Positives = 19/34 (55%), Gaps = 4/34 (11%)
Query: 159 GDFPGCEDIEGMV-IPSVGRKISNIVMM-GMGEP 190
G+ P ED + +P VGRK +N+V+ G P
Sbjct: 80 GEVP--EDRAALEALPGVGRKTANVVLNTAFGWP 111
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
0.323 0.140 0.421
Gapped
Lambda K H
0.267 0.0710 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 33805
Number of Hits to DB: 2,965,366
Number of extensions: 137535
Number of successful extensions: 314
Number of sequences better than 10.0: 1
Number of HSP's gapped: 309
Number of HSP's successfully gapped: 23
Length of query: 384
Length of database: 4,956,049
Length adjustment: 90
Effective length of query: 294
Effective length of database: 1,913,599
Effective search space: 562598106
Effective search space used: 562598106
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 (21.9 bits)
S2: 55 (25.0 bits)