RPS-BLAST 2.2.22 [Sep-27-2009]

Database: pdb70 
           24,244 sequences; 5,693,230 total letters

Searching..................................................done

Query= gi|254781120|ref|YP_003065533.1| radical SAM protein
[Candidatus Liberibacter asiaticus str. psy62]
         (384 letters)



>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 = 52.6 bits (126), Expect = 1e-07
 Identities = 74/406 (18%), Positives = 116/406 (28%), Gaps = 161/406 (39%)

Query: 20  ALLKIGIPQRHVRMRTSQIWKWIYVRGIRDF--QG-MSDISQEVRHLLNQHFSIIYPEIV 76
           AL       R V    +Q+        I  F  QG   D  +E+R L        Y  +V
Sbjct: 144 ALF------RAVGEGNAQL----VA--I--FGGQGNTDDYFEELRDLYQ-----TYHVLV 184

Query: 77  DEKISCDGTRKWLLRFPARCIGGPVEIETVYI-----------PEK--SRGTLCVSSQVG 123
            + I        L     R     ++ E V+            P     +  L +S  + 
Sbjct: 185 GDLIKFSAET--LSEL-IRT---TLDAEKVFTQGLNILEWLENPSNTPDKDYL-LSIPIS 237

Query: 124 CSL-----------TC------------SFC-YTG-TQKLVRNLTA---------EEILL 149
           C L           T                  TG +Q LV   TA         E   +
Sbjct: 238 CPLIGVIQLAHYVVTAKLLGFTPGELRSYLKGATGHSQGLV---TAVAIAETDSWESFFV 294

Query: 150 QVLLARSLLGDF-PGCEDIEG---MVIPSVGRK--ISNIVMMGMGEPLCNFDNVKKS--L 201
            V  A ++L  F  G    E      +P    +  + N      G P         S  L
Sbjct: 295 SVRKAITVL--FFIGVRCYEAYPNTSLPPSILEDSLEN----NEGVP---------SPML 339

Query: 202 SIASDSMGLSFSK--RRITLSTSGFVP----------NIAR---VGEEIGVMLAISLHAV 246
           SI+     L+  +    +   T+  +P          N A+   V    G     SL+ +
Sbjct: 340 SIS----NLTQEQVQDYVN-KTNSHLPAGKQVEISLVNGAKNLVVS---G--PPQSLYGL 389

Query: 247 SNDLRNILVPIN----------RKYPLEM--L-IDACRHYPGLSNARRITFEYVMLKGIN 293
           +  LR    P            RK       L + +  H   L  A  +  + ++   ++
Sbjct: 390 NLTLRKAKAPSGLDQSRIPFSERKLKFSNRFLPVASPFHSHLLVPASDLINKDLVKNNVS 449

Query: 294 DSPRDALNLIKI-------------LKG--IPAKINLIPFNP--WP 322
            + +D    I+I             L G      ++ I   P  W 
Sbjct: 450 FNAKD----IQIPVYDTFDGSDLRVLSGSISERIVDCIIRLPVKWE 491



 Score = 31.1 bits (70), Expect = 0.42
 Identities = 46/287 (16%), Positives = 77/287 (26%), Gaps = 109/287 (37%)

Query: 119 SSQVGCSLTCSF-CYTGTQKLVRNLTAEEILLQVLLA---RSLLGDFPGCEDIEGMV--- 171
           ++     L   F  Y  +      +   + +L + L       L       DI  +    
Sbjct: 55  TTPAE--LVGKFLGYVSSLVEPSKVGQFDQVLNLCLTEFENCYLEG----NDIHALAAKL 108

Query: 172 ---IPSVGRKISNIVMMGMGEPLCNFDNVKKSLSIASDSMGLSFSKRRITLSTSGFVPNI 228
                +   K   +        + N+         A       F K+    S S      
Sbjct: 109 LQENDTTLVKTKEL--------IKNYIT-------ARIMAKRPFDKK----SNSALF-RA 148

Query: 229 ARVGEEIGVMLAISLHAV------SND----LRNILVPINRKYP--LEMLIDAC-RHYPG 275
              G          L A+      ++D    LR++     + Y   +  LI         
Sbjct: 149 VGEGN-------AQLVAIFGGQGNTDDYFEELRDL----YQTYHVLVGDLIKFSAETLSE 197

Query: 276 LSNARRITFEYVMLKGINDSPRDALNLIKILKGIPAKINLIPFNPWPGCEYLCSDQKDIV 335
           L     +  E V  +G        LN+++ L+  P+          P  +YL        
Sbjct: 198 LI-RTTLDAEKVFTQG--------LNILEWLEN-PSNT--------PDKDYLL------- 232

Query: 336 TFSECIKRSGYSSPIRTPR-GLDILA----AC-------GQLKS-LS 369
                      S PI  P  G+  LA             G+L+S L 
Sbjct: 233 -----------SIPISCPLIGVIQLAHYVVTAKLLGFTPGELRSYLK 268



 Score = 29.5 bits (66), Expect = 1.1
 Identities = 59/279 (21%), Positives = 100/279 (35%), Gaps = 104/279 (37%)

Query: 34   RTSQIWKWIYVRG---IRDFQGMSDISQEVRHLLNQ--HF-------------SIIYPEI 75
            +TS+  + ++ R     +D  G S +   + + +N   HF             ++I+  I
Sbjct: 1637 KTSKAAQDVWNRADNHFKDTYGFSILDIVINNPVNLTIHFGGEKGKRIRENYSAMIFETI 1696

Query: 76   VDEKISCDG---------------TRKWLL---RF--PARCIGGPVEIETVYIPEKSRGT 115
            VD K+  +                + K LL   +F  PA  +      E +    KS+G 
Sbjct: 1697 VDGKLKTEKIFKEINEHSTSYTFRSEKGLLSATQFTQPALTLMEKAAFEDL----KSKGL 1752

Query: 116  LCVSSQ-VGCSLTCSFCYTGTQKLVRNLTAEEILLQVLLARSLLGDFPGCEDIEGMV--- 171
            +   +   G SL     Y     L   ++ E  L++V+  R             GM    
Sbjct: 1753 IPADATFAGHSLGE---YAALASLADVMSIES-LVEVVFYR-------------GMTMQV 1795

Query: 172  -IP--SVGRKISNIVMMGMGEPLCNFDNVKKSLSIASDSMGLSFSKRRITLSTSGFVPNI 228
             +P   +GR  SN    GM             ++I    +  SFS+  +      +V  +
Sbjct: 1796 AVPRDELGR--SN---YGM-------------IAINPGRVAASFSQEALQ-----YV--V 1830

Query: 229  ARVGEEIGVMLAISLHAVSN-------DLR------NIL 254
             RVG+  G ++ I  + V N       DLR      N+L
Sbjct: 1831 ERVGKRTGWLVEIVNYNVENQQYVAAGDLRALDTVTNVL 1869


>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*
          Length = 245

 Score = 49.2 bits (116), Expect = 1e-06
 Identities = 36/206 (17%), Positives = 74/206 (35%), Gaps = 38/206 (18%)

Query: 123 GCSLTCSFCY---TGTQKLVRNLTAEEILLQVLLARSLLGDFPGCEDIEGMVIPSVGRKI 179
           GC + C +C+   T      + +T E+++ +V+  R  +    G                
Sbjct: 28  GCLMRCLYCHNRDTWDTHGGKEVTVEDLMKEVVTYRHFMNASGGG--------------- 72

Query: 180 SNIVMMGMGEPLCNFDNVKKSLSIASDSMGLSFSKRRITLSTSGFVPNIARVGEE---IG 236
              V    GE +   + V+                    L T+GFV     V +E   + 
Sbjct: 73  ---VTASGGEAILQAEFVRDWFRACKKEG------IHTCLDTNGFVRRYDPVIDELLEVT 123

Query: 237 VMLAISLHAVSNDLRNILVPINRKYPLEMLIDACRHYPGLSNARRITFEYVMLKGINDSP 296
            ++ + L  +++++   LV ++    LE                ++   YV++ G +D  
Sbjct: 124 DLVMLDLKQMNDEIHQNLVGVSNHRTLEFAKYLANKNV------KVWIRYVVVPGWSDDD 177

Query: 297 RDALNLIKILKGIPA--KINLIPFNP 320
             A  L +  + +    KI L+P++ 
Sbjct: 178 DSAHRLGEFTRDMGNVEKIELLPYHE 203


>2yx0_A Radical SAM enzyme; predicted tRNA modification enzyme, metal
           binding protein, structural genomics, NPPSFA; 2.21A
           {Pyrococcus horikoshii}
          Length = 342

 Score = 42.4 bits (99), Expect = 2e-04
 Identities = 28/210 (13%), Positives = 57/210 (27%), Gaps = 21/210 (10%)

Query: 123 GCSLTCSFCY------TGTQKLVRNLTAEEILLQVLLARSLLGDFPGCEDIEGMVIPSVG 176
            C+  C FC+       GT+          I+ + + A+  L                  
Sbjct: 80  WCTHNCIFCWRPMENFLGTELPQPWDDPAFIVEESIKAQRKLLIGYKGNPKVDKKKFEEA 139

Query: 177 RKISNIVMMGMGEPLCNFDNVKKSLSIASDSMGLSFSKRRITLSTSGFVPNIARVGEEIG 236
              ++  +   GEP+                           + T+G +P       +  
Sbjct: 140 WNPTHAAISLSGEPMLYPYMGDLVEEFHKRGF-------TTFIVTNGTIPERLEEMIKED 192

Query: 237 ---VMLAISLHAVSNDLRNILVPINRKYPLEMLIDACRHYPGLSNAR-RITFEYVMLKGI 292
                L +S+ A   +  N +         E ++        + +   R      ++KG 
Sbjct: 193 KLPTQLYVSITAPDIETYNSVNIPMIPDGWERILRFLEL---MRDLPTRTVVRLTLVKGE 249

Query: 293 NDS-PRDALNLIKILKGIPAKINLIPFNPW 321
           N   P     LI   + +  +     F  +
Sbjct: 250 NMHSPEKYAKLILKARPMFVEAKAYMFVGY 279


>2z2u_A UPF0026 protein MJ0257; metal binding protein; 2.40A
           {Methanocaldococcus jannaschii}
          Length = 311

 Score = 40.1 bits (93), Expect = 8e-04
 Identities = 30/214 (14%), Positives = 66/214 (30%), Gaps = 30/214 (14%)

Query: 120 SQVGCSLTCSFCYTGTQKLV----------RNLTAEEILLQVL-LARSLLGDFPGCEDIE 168
           S + C   C FC+    + +          +    E +  ++L + + ++  + G  D  
Sbjct: 58  SVIWCQQNCIFCWRVLPRDIGIDISQIKEPKWEEPEVVYEKILAMHKRIIMGYAGVLDRV 117

Query: 169 GMVIPSVGRKISNIVMMGMGEPLCNFDNVKKSLSIASDSMGLSFSKRRITLSTSGFVPNI 228
           G        +  ++ +   GEP       +    +        F+   ++          
Sbjct: 118 GEKKFKEALEPKHVAISLSGEPTLYPYLDE----LIKIFHKNGFTTFVVSNGI-----LT 168

Query: 229 ARVGEEIGVMLAISLHAVSND-LRNILVPINRKYPLEML-IDACRHYPGLSNARRITFEY 286
             + +     L ISL A   D  R I       +   +  +D  +        +R     
Sbjct: 169 DVIEKIEPTQLYISLDAYDLDSYRRICGGKKEYWESILNTLDILK------EKKRTCIRT 222

Query: 287 VMLKGINDSPRDALNLIKILKGIPAKINLIPFNP 320
            +++G ND     + L +  +     I L  +  
Sbjct: 223 TLIRGYNDDILKFVELYE--RADVHFIELKSYMH 254


>3cux_A Malate synthase; TIM barrel, glyoxylate bypass, transferase,
           tricarboxylic acid cycle; 1.70A {Bacillus anthracis}
          Length = 528

 Score = 29.6 bits (66), Expect = 1.3
 Identities = 11/51 (21%), Positives = 21/51 (41%)

Query: 31  VRMRTSQIWKWIYVRGIRDFQGMSDISQEVRHLLNQHFSIIYPEIVDEKIS 81
             +  +Q+W+WI   G +   G +   + +  L  +  + I  EI  E   
Sbjct: 446 AEISRAQVWQWIRHEGGKLNDGRNITLELMEELKEEELAKIEREIGKEAFK 496


>3fho_A ATP-dependent RNA helicase DBP5; mRNA export, ATPase, translation
           termination, ATP-binding, cytoplasm, hydrolase,
           membrane; 2.80A {Schizosaccharomyces pombe}
          Length = 508

 Score = 29.3 bits (65), Expect = 1.7
 Identities = 18/73 (24%), Positives = 34/73 (46%), Gaps = 13/73 (17%)

Query: 19  EALLKIGIP--------QRHVRMRTSQIWKWIYVRGIRDFQGMSDISQEVRHLLNQH--- 67
           +A + IG P        +R +  R  +++       + D QG+ D S  ++HLL ++   
Sbjct: 235 DAQIVIGTPGTVMDLMKRRQLDARDIKVFVLDEADNMLDQQGLGDQSMRIKHLLPRNTQI 294

Query: 68  --FSIIYPEIVDE 78
             FS  + E V++
Sbjct: 295 VLFSATFSERVEK 307


>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}
          Length = 416

 Score = 27.7 bits (61), Expect = 4.7
 Identities = 23/143 (16%), Positives = 49/143 (34%), Gaps = 12/143 (8%)

Query: 215 RRITLSTSGFVPNIARVGEEIGVMLAISLHAVSNDLRNILVPINRKYPLEMLIDACRHYP 274
             + + +   V    R+  E        L  +      + +  +  +P E+  ++ R   
Sbjct: 195 EIVRIGSRTPVVLPQRITPE--------LVNMLKKYHPVWLNTHFNHPNEITEESTRACQ 246

Query: 275 GLSNAR-RITFEYVMLKGINDSPRDALNLIKILKGIPAK-INLIPFNPWPGCEYLCSDQK 332
            L++A   +  + V+L+G+ND       L+  L  I  +   +   +   G E+  +   
Sbjct: 247 LLADAGVPLGNQSVLLRGVNDCVHVMKELVNKLVKIRVRPYYIYQCDLSLGLEHFRTPVS 306

Query: 333 DIVTF--SECIKRSGYSSPIRTP 353
             +          SGY  P    
Sbjct: 307 KGIEIIEGLRGHTSGYCVPTFVV 329


  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
   0.323    0.140    0.421 

Gapped
Lambda     K      H
   0.267   0.0521    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 3,396,284
Number of extensions: 162897
Number of successful extensions: 426
Number of sequences better than 10.0: 1
Number of HSP's gapped: 422
Number of HSP's successfully gapped: 16
Length of query: 384
Length of database: 5,693,230
Length adjustment: 94
Effective length of query: 290
Effective length of database: 3,414,294
Effective search space: 990145260
Effective search space used: 990145260
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: 57 (26.2 bits)