RPS-BLAST 2.2.22 [Sep-27-2009]

Database: CddA 
           21,609 sequences; 6,263,737 total letters

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

Query= gi|254780676|ref|YP_003065089.1| lipoyl synthase [Candidatus
Liberibacter asiaticus str. psy62]
         (329 letters)



>gnl|CDD|30668 COG0320, LipA, Lipoate synthase [Coenzyme metabolism].
          Length = 306

 Score =  486 bits (1253), Expect = e-138
 Identities = 179/302 (59%), Positives = 217/302 (71%)

Query: 21  AERLRHPEKIHKPDTEKMQKPDWIRVRAPVSSGYKETYNILRSRNLTTVCEEAGCPNIGE 80
            +  R P K  +P+ E ++KP+W++V+AP  S Y+E   ILR   L TVCEEA CPNIGE
Sbjct: 5   DKMARIPVKNVRPNEELLRKPEWLKVKAPTGSRYQEIKEILRKNGLHTVCEEASCPNIGE 64

Query: 81  CWNKNHATFMILGAICTRACTFCNVATGKPQPLDPQEPENISWAVRSMKLSHVVITSVDR 140
           CW++  ATFMILG ICTR C FC+V TG+P PLDP EPE ++ AV+ M L +VVITSVDR
Sbjct: 65  CWSRGTATFMILGDICTRRCRFCDVKTGRPNPLDPDEPERVAEAVKDMGLKYVVITSVDR 124

Query: 141 DDLDDGGAQHFAEVISAIRESAPSTTIEVLTPDFLRKPHALEKVVSAKPDVFNHNLETVA 200
           DDL DGGAQHFAE I AIRE  P TTIEVLTPDF     ALE V  A PDVFNHN+ETV 
Sbjct: 125 DDLPDGGAQHFAECIRAIRELNPQTTIEVLTPDFRGNDDALEIVADAGPDVFNHNVETVP 184

Query: 201 SNYLMVRPGARYFHSLRLLQRVKELDPLIFTKSGIMLGLGETRNEILQLMDDLRTADVDF 260
             Y  VRPGA Y  SL LL+R KEL P I TKSG+M+GLGET  E++++MDDLR+A VD 
Sbjct: 185 RLYPRVRPGATYERSLSLLERAKELGPDIPTKSGLMVGLGETDEEVIEVMDDLRSAGVDI 244

Query: 261 LTMGQYLQPTRKHHKVESFVTPQDFKSYETIAYSKGFLMVSASPLTRSSYHAGDDFLRLK 320
           LT+GQYLQP+RKH  V+ +VTP++F   E +A   GFL V++ PL RSSYHA + F   +
Sbjct: 245 LTIGQYLQPSRKHLPVQRYVTPEEFDELEEVAEEMGFLHVASGPLVRSSYHADEQFAEAE 304

Query: 321 NN 322
             
Sbjct: 305 VK 306


>gnl|CDD|37883 KOG2672, KOG2672, KOG2672, Lipoate synthase [Coenzyme transport and
           metabolism].
          Length = 360

 Score =  312 bits (800), Expect = 9e-86
 Identities = 140/290 (48%), Positives = 185/290 (63%), Gaps = 7/290 (2%)

Query: 36  EKMQKPDWIRVRAPVSSGYKETYNILRSRNLTTVCEEAGCPNIGECWN-----KNHATFM 90
           E+++ P W++ + P+   Y +    LR   L TVCEEA CPNIGECW         AT M
Sbjct: 56  ERLRLPPWLKTKIPLGENYNKIKKDLRELKLHTVCEEARCPNIGECWGGGDKSTATATIM 115

Query: 91  ILGAICTRACTFCNVATGK-PQPLDPQEPENISWAVRSMKLSHVVITSVDRDDLDDGGAQ 149
           ++G  CTR C FC+V T + P PLDP EPEN + A+ S  L ++V+TSVDRDDL DGGA 
Sbjct: 116 LMGDTCTRGCRFCSVKTSRNPPPLDPNEPENTAEAIASWGLDYIVLTSVDRDDLPDGGAN 175

Query: 150 HFAEVISAIRESAPSTTIEVLTPDFLRKPHALEKVVSAKPDVFNHNLETVASNYLMVR-P 208
           H A+ +  I+E AP   +E LTPDF     A+EKV  +  DV+ HN+ETV      VR P
Sbjct: 176 HIAKTVQKIKEKAPEILVECLTPDFRGDLKAVEKVAKSGLDVYAHNVETVEELTPFVRDP 235

Query: 209 GARYFHSLRLLQRVKELDPLIFTKSGIMLGLGETRNEILQLMDDLRTADVDFLTMGQYLQ 268
            A Y  SL +L+  KE+ P + TK+ IMLGLGET  EI Q + DLR ADVD +T GQY+Q
Sbjct: 236 RANYRQSLSVLKHAKEVKPGLITKTSIMLGLGETDEEIKQTLKDLRAADVDVVTFGQYMQ 295

Query: 269 PTRKHHKVESFVTPQDFKSYETIAYSKGFLMVSASPLTRSSYHAGDDFLR 318
           PT++H KV+ +VTP+ F  ++      GFL V++ PL RSSY AG+ F++
Sbjct: 296 PTKRHLKVKEYVTPEKFDYWKEYGEELGFLYVASGPLVRSSYKAGEYFIK 345


>gnl|CDD|146602 pfam04055, Radical_SAM, Radical SAM superfamily.  Radical SAM
           proteins catalyse diverse reactions, including unusual
           methylations, isomerisation, sulphur insertion, ring
           formation, anaerobic oxidation and protein radical
           formation.
          Length = 165

 Score = 79.1 bits (195), Expect = 1e-15
 Identities = 33/169 (19%), Positives = 65/169 (38%), Gaps = 9/169 (5%)

Query: 90  MILGAICTRACTFCNV----ATGKPQPLDPQEPENISWAVRSMKLSHVVITSVDRDDLDD 145
           +I+   C   CT+C      A GK + L P+E    +  +  + +  V++T  +   L D
Sbjct: 1   IIITPGCNLRCTYCAFPSIRARGKGRELSPEEILEEAKELARLGVEVVILTGGEPLLLPD 60

Query: 146 GGAQHFAEVISAIRESAPSTTIEVLTPDFLRKPHALEKVVSAKPDVFNHNLETVASNYL- 204
                         E      I + T   L     LE++  A  D  + +L++     L 
Sbjct: 61  LVELLERL---LKLEELEGIRITLETNGTLLDEELLEELKEAGLDRVSISLQSGDDEVLK 117

Query: 205 MVRPGARYFHSLRLLQRVKELDPLIFTKSGIMLGLGETRNEILQLMDDL 253
           ++  G  +   L  L+ ++E   +      I+   GE   ++ + ++ L
Sbjct: 118 IINRGHTFEEVLEALELLREAG-IPVVVDNIVGLPGENDEDLEETLELL 165


>gnl|CDD|30848 COG0502, BioB, Biotin synthase and related enzymes [Coenzyme
           metabolism].
          Length = 335

 Score = 57.6 bits (139), Expect = 5e-09
 Identities = 42/168 (25%), Positives = 66/168 (39%), Gaps = 13/168 (7%)

Query: 96  CTRACTFCNVATGKPQPLDPQ---EPENISWAVRSMK---LSHVVITSVDRDDLDDGGAQ 149
           C   C +C+ +      +  +   E E I  A +  K    +   + +  R    D    
Sbjct: 61  CPEDCAYCSQSARYKTGVKARKLMEVEEILEAAKKAKAAGATRFCMGAAGRGPGRD---- 116

Query: 150 HFAEVISAIRESAPSTTIEVLTPDFLRKPHALEKVVSAKPDVFNHNLETVASNYLMVRPG 209
              EV+ AI+       +EV     +      EK+  A  D +NHNLET    Y  +   
Sbjct: 117 -MEEVVEAIKAVKEELGLEVCASLGMLTEEQAEKLADAGVDRYNHNLETSPEFYENIITT 175

Query: 210 ARYFHSLRLLQRVKELDPLIFTKSGIMLGLGETRNEILQLMDDLRTAD 257
             Y   L  L+ V+E    I   SG ++GLGET  +  +L+ +L    
Sbjct: 176 RTYEDRLNTLENVREAG--IEVCSGGIVGLGETVEDRAELLLELANLP 221


>gnl|CDD|100105 cd01335, Radical_SAM, Radical SAM superfamily. Enzymes of this
           family generate radicals by combining a 4Fe-4S cluster
           and S-adenosylmethionine (SAM) in close proximity. They
           are characterized by a conserved CxxxCxxC motif, which
           coordinates the conserved iron-sulfur cluster.
           Mechanistically, they share the transfer of a single
           electron from the iron-sulfur cluster to SAM, which
           leads to its reductive cleavage to methionine and a
           5'-deoxyadenosyl radical, which, in turn, abstracts a
           hydrogen from the appropriately positioned carbon atom.
           Depending on the enzyme, SAM is consumed during this
           process or it is restored and reused. Radical SAM
           enzymes catalyze steps in metabolism, DNA repair, the
           biosynthesis of vitamins and coenzymes, and the
           biosynthesis of many antibiotics. Examples are biotin
           synthase (BioB), lipoyl synthase (LipA), pyruvate
           formate-lyase (PFL), coproporphyrinogen oxidase (HemN),
           lysine 2,3-aminomutase (LAM), anaerobic ribonucleotide
           reductase (ARR), and  MoaA, an enzyme of the
           biosynthesis of molybdopterin..
          Length = 204

 Score = 56.2 bits (135), Expect = 1e-08
 Identities = 32/186 (17%), Positives = 72/186 (38%), Gaps = 15/186 (8%)

Query: 90  MILGAICTRACTFCNVATGK----PQPLDPQEPENISWAVRSMKLSHVVITSVDRDDLDD 145
           + L   C   C FC+    K      P + +E  +I    +   +  V++T  +      
Sbjct: 1   LELTRGCNLNCGFCSNPASKGRGPESPPEIEEILDIVLEAKERGVEVVILTGGEPLLYP- 59

Query: 146 GGAQHFAEVISAIRESAPSTTIEVLTPDFLRKPHALEKVVSAKPDVFNHNLETV--ASNY 203
                 AE++  +++  P   I + T   L     L+++     D    +L++       
Sbjct: 60  ----ELAELLRRLKKELPGFEISIETNGTLLTEELLKELKELGLDGVGVSLDSGDEEVAD 115

Query: 204 LMVRPGARYFHSLRLLQRVKELDPLIFTKSGIMLGLG-ETRNEILQLMDDLRTAD-VDFL 261
            +   G  +   L  L+ ++E    +   + +++GLG E   + L+ ++ L      D +
Sbjct: 116 KIRGSGESFKERLEALKELREAG--LGLSTTLLVGLGDEDEEDDLEELELLAEFRSPDRV 173

Query: 262 TMGQYL 267
           ++ + L
Sbjct: 174 SLFRLL 179


>gnl|CDD|31260 COG1060, ThiH, Thiamine biosynthesis enzyme ThiH and related
           uncharacterized enzymes [Coenzyme metabolism / General
           function prediction only].
          Length = 370

 Score = 41.0 bits (96), Expect = 4e-04
 Identities = 44/221 (19%), Positives = 80/221 (36%), Gaps = 39/221 (17%)

Query: 95  ICTRACTFCNVATGKPQP----LDPQEPENISWAVRSMKLSHVVITSVDRDDLDDGGAQH 150
           IC   CTFC        P    L P+E            ++ V+I   +  +L     ++
Sbjct: 68  ICVNDCTFCAFYRKPGDPKAYTLSPEEILEEVREAVKRGITEVLIVGGEHPELS---LEY 124

Query: 151 FAEVISAIRESAPSTTIEVLTPDFLRKPHALEKVVSAKPDVF----NHNLETV---ASNY 203
           + E+   I+E  P   I  L+   +    A E  +S + +V        L+++    +  
Sbjct: 125 YEELFRTIKEEFPDLHIHALSAGEIL-FLAREGGLSYE-EVLKRLKEAGLDSMPGGGAEI 182

Query: 204 LM--VR-----PGARYFHSLRLLQRVKELDPLIFTKSGIMLGLGETRNEILQLMDDLRTA 256
           L   VR     P       L + +R   L   I T + ++LG  ETR + +  ++ +R  
Sbjct: 183 LSEEVRKIHCPPKKSPEEWLEIHERAHRLG--IPTTATMLLGHVETREDRIDHLEHIR-- 238

Query: 257 DVDFLTMGQYLQPTRKHHKVESFVTPQDFKSYETIAYSKGF 297
                     LQ   +    + F+ P  F+       ++  
Sbjct: 239 ---------DLQ--DETGGFQEFI-PLRFRPENGPLPAEVV 267


>gnl|CDD|35762 KOG0542, KOG0542, KOG0542, Predicted exonuclease [Replication,
           recombination and repair].
          Length = 280

 Score = 30.3 bits (68), Expect = 0.85
 Identities = 10/43 (23%), Positives = 16/43 (37%)

Query: 37  KMQKPDWIRVRAPVSSGYKETYNILRSRNLTTVCEEAGCPNIG 79
            ++ P +      +   YK  YN     N+T + E  G    G
Sbjct: 177 NIRIPAFFNQWINIRKIYKNFYNRPAPTNITGMLEHYGLQFEG 219


>gnl|CDD|30966 COG0621, MiaB, 2-methylthioadenine synthetase [Translation,
           ribosomal structure and biogenesis].
          Length = 437

 Score = 29.4 bits (66), Expect = 1.4
 Identities = 40/186 (21%), Positives = 78/186 (41%), Gaps = 20/186 (10%)

Query: 96  CTRACTFCNV--ATGKPQPLDPQEPENISWAVRSMKLS---HVVITSVD----RDDLDDG 146
           C + CTFC +  A GK      + PE+I   V+ +       +V+T  D      DL  G
Sbjct: 154 CNKFCTFCIIPYARGK---ERSRPPEDILKEVKRLVAQGVKEIVLTGQDVNAYGKDLGGG 210

Query: 147 GAQHFAEVISAIRESAPSTTIEVLTPDFLRKPHALEKVVSAKPDVFNH---NLETVASNY 203
              + A+++  + +      I   +   L     L + ++  P V  H    +++ +   
Sbjct: 211 KP-NLADLLRELSKIPGIERIRFGSSHPLEFTDDLIEAIAETPKVCPHLHLPVQSGSDRI 269

Query: 204 L--MVRPGARYFHSLRLLQRVKELDPLIFTKSGIMLGL-GETRNEILQLMDDLRTADVDF 260
           L  M R      + L ++++++   P I   + I++G  GET  +  + +D +     D 
Sbjct: 270 LKRMKRGYTVEEY-LEIIEKLRAARPDIAISTDIIVGFPGETEEDFEETLDLVEEVRFDR 328

Query: 261 LTMGQY 266
           L + +Y
Sbjct: 329 LHVFKY 334


>gnl|CDD|73367 cd00564, TMP_TenI, Thiamine monophosphate synthase (TMP
           synthase)/TenI. TMP synthase catalyzes an important step
           in the thiamine biosynthesis pathway, the substitution
           of the pyrophosphate of 2-methyl-4-amino-5-
           hydroxymethylpyrimidine pyrophosphate by 4-methyl-5-
           (beta-hydroxyethyl) thiazole phosphate to yield thiamine
           phosphate. TenI is a enzymatically inactive regulatory
           protein involved in the regulation of several
           extracellular enzymes. This superfamily also contains
           other enzymatically inactive proteins with unknown
           functions..
          Length = 196

 Score = 29.4 bits (66), Expect = 1.6
 Identities = 14/53 (26%), Positives = 22/53 (41%), Gaps = 4/53 (7%)

Query: 109 KPQPLDPQEPENISWAVRSMKLSHVVITSVDRDDLDD---GGAQHFAEVISAI 158
           KP    P   E +      +++  V I  +  ++  +    GA   A VISAI
Sbjct: 130 KPGAGPPLGLELLREIAELVEIPVVAIGGITPENAAEVLAAGADGVA-VISAI 181


>gnl|CDD|32379 COG2197, CitB, Response regulator containing a CheY-like receiver
           domain and an HTH DNA-binding domain [Signal
           transduction mechanisms / Transcription].
          Length = 211

 Score = 29.2 bits (65), Expect = 1.9
 Identities = 19/102 (18%), Positives = 38/102 (37%), Gaps = 6/102 (5%)

Query: 152 AEVISAIRESAPSTTIEVLTPDFLRKPHALEKVVSAKPDVFNH---NLETVASNYLMVRP 208
            E +  +R   P   + VLT      P  + + + A  D +     + E +      V  
Sbjct: 62  LEALKQLRARGPDIKVVVLTAHD--DPAYVIRALRAGADGYLLKDASPEELVEAIRAVAA 119

Query: 209 GARYFHSLRLLQRVKELDPLIFTKSGIMLGLGETRNEILQLM 250
           G  Y     + +++  L P    ++ +   L     E+L+L+
Sbjct: 120 GGTYLPP-DIARKLAGLLPSSSAEAPLAELLTPRELEVLRLL 160


>gnl|CDD|38111 KOG2900, KOG2900, KOG2900, Biotin synthase [Coenzyme transport and
           metabolism].
          Length = 380

 Score = 28.5 bits (63), Expect = 2.8
 Identities = 22/64 (34%), Positives = 34/64 (53%), Gaps = 2/64 (3%)

Query: 192 FNHNLETVASNYLMVRPGARYFHSLRLLQRVKELDPLIFTKSGIMLGLGETRNEILQLMD 251
           +NHNL+T    Y  V     Y   L+ ++ V+E    I   SG +LGLGE+ ++ + L+ 
Sbjct: 193 YNHNLDTSREYYSKVITTRTYDDRLQTIKNVREAG--IKVCSGGILGLGESEDDRIGLIH 250

Query: 252 DLRT 255
            L T
Sbjct: 251 TLAT 254


>gnl|CDD|176152 cd08463, PBP2_DntR_like_4, The C-terminal substrate binding domain
           of an uncharacterized LysR-type transcriptional
           regulator similar to DntR, which is involved in the
           catabolism of dinitrotoluene; contains the type 2
           periplasmic binding fold.  This CD includes an
           uncharacterized LysR-type transcriptional regulator
           similar to DntR, NahR, and LinR, which are involved in
           the degradation of aromatic compounds. The transcription
           of the genes encoding enzymes involved in such
           degradation is regulated and expression of these enzymes
           is enhanced by inducers, which are either an
           intermediate in the metabolic pathway or compounds to be
           degraded.  This substrate-binding domain shows
           significant homology to the type 2 periplasmic binding
           proteins (PBP2), which are responsible for the uptake of
           a variety of substrates such as phosphate, sulfate,
           polysaccharides, lysine/arginine/ornithine, and
           histidine. The PBP2 bind their ligand in the cleft
           between these domains in a manner resembling a Venus
           flytrap. After binding their specific ligand with high
           affinity, they can interact with a cognate membrane
           transport complex comprised of two integral membrane
           domains and two cytoplasmically located ATPase domains.
           This interaction triggers the ligand translocation
           across the cytoplasmic membrane energized by ATP
           hydrolysis.
          Length = 203

 Score = 27.7 bits (62), Expect = 4.3
 Identities = 12/38 (31%), Positives = 17/38 (44%), Gaps = 3/38 (7%)

Query: 147 GAQHFAEVISAIRESAPSTTIEV--LTPDFLRKPHALE 182
            A    E+++  R  AP   +E+  L PDF     AL 
Sbjct: 11  NALFLPELVARFRREAPGARLEIHPLGPDF-DYERALA 47


>gnl|CDD|39700 KOG4500, KOG4500, KOG4500, Rho/Rac GTPase guanine nucleotide
           exchange factor smgGDS/Vimar [Signal transduction
           mechanisms].
          Length = 604

 Score = 27.4 bits (60), Expect = 5.8
 Identities = 16/49 (32%), Positives = 23/49 (46%)

Query: 216 LRLLQRVKELDPLIFTKSGIMLGLGETRNEILQLMDDLRTADVDFLTMG 264
           L L +R+ ELD L+ T    M  L      +  L    R+ D + +TMG
Sbjct: 287 LNLFKRIAELDVLLLTGDESMQKLHADPQFLDFLESWFRSDDSNLITMG 335


>gnl|CDD|30911 COG0565, LasT, rRNA methylase [Translation, ribosomal structure and
           biogenesis].
          Length = 242

 Score = 26.7 bits (59), Expect = 7.9
 Identities = 13/52 (25%), Positives = 23/52 (44%), Gaps = 7/52 (13%)

Query: 114 DPQEPENISWAVRSMK---LSHVVITSVDRDDLDD---GGAQHFAEVISAIR 159
           +P  P NI    R+MK   LS + + +  R  LD+     A    +++   +
Sbjct: 11  EPSHPGNIGSVARAMKNFGLSELRLVN-PRAGLDEEARALAAGARDILENAK 61


>gnl|CDD|30059 cd01316, CAD_DHOase, The eukaryotic CAD protein is a trifunctional
           enzyme of carbamoylphosphate synthetase-aspartate
           transcarbamoylase-dihydroorotase, which catalyzes the
           first three steps of de novo pyrimidine nucleotide
           biosynthesis. Dihydroorotase (DHOase) catalyzes the
           third step, the reversible interconversion of carbamoyl
           aspartate to dihydroorotate..
          Length = 344

 Score = 26.8 bits (59), Expect = 8.2
 Identities = 12/48 (25%), Positives = 18/48 (37%)

Query: 281 TPQDFKSYETIAYSKGFLMVSASPLTRSSYHAGDDFLRLKNNRRQHLH 328
             +DF S    A + GF MV A P T  S         +++  +    
Sbjct: 22  HKEDFASGTKAALAGGFTMVRAMPNTNPSIVDVASLKLVQSLAQAKAR 69


>gnl|CDD|30955 COG0610, COG0610, Type I site-specific restriction-modification
           system, R (restriction) subunit and related helicases
           [Defense mechanisms].
          Length = 962

 Score = 26.9 bits (59), Expect = 8.3
 Identities = 11/48 (22%), Positives = 16/48 (33%), Gaps = 1/48 (2%)

Query: 123 WAVRSMKLSHVVITSVDRDDLDDGGAQHFAEVISAIRESAPSTTIEVL 170
             +   K   V+   VDR DLDD  +  F            + +   L
Sbjct: 296 LLLELPKNPKVLFV-VDRKDLDDQTSDEFQSFGKVAFNDPKAESTSEL 342


>gnl|CDD|36773 KOG1560, KOG1560, KOG1560, Translation initiation factor 3, subunit
           h (eIF-3h) [Translation, ribosomal structure and
           biogenesis].
          Length = 339

 Score = 26.5 bits (58), Expect = 9.8
 Identities = 20/81 (24%), Positives = 32/81 (39%), Gaps = 20/81 (24%)

Query: 241 ETRNEILQLMDDLRTADVDFLTMGQYLQPTRKHHKVESFVTPQDFKS------------- 287
             +   L ++  LR  ++D L +G Y         V SF++P   +S             
Sbjct: 79  ARQAYQLAMLRRLRYVNIDHLHVGWYQS-----AYVGSFLSPALVESQYAYQKAIPESVV 133

Query: 288 --YETIAYSKGFLMVSASPLT 306
             Y+ I  S+G L + A  LT
Sbjct: 134 LIYDPIKSSQGTLSLRAYRLT 154


  Database: CddA
    Posted date:  Feb 4, 2011  9:38 PM
  Number of letters in database: 6,263,737
  Number of sequences in database:  21,609
  
Lambda     K      H
   0.320    0.134    0.402 

Gapped
Lambda     K      H
   0.267   0.0623    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 4,063,824
Number of extensions: 211833
Number of successful extensions: 458
Number of sequences better than 10.0: 1
Number of HSP's gapped: 453
Number of HSP's successfully gapped: 23
Length of query: 329
Length of database: 6,263,737
Length adjustment: 94
Effective length of query: 235
Effective length of database: 4,232,491
Effective search space: 994635385
Effective search space used: 994635385
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: 58 (26.3 bits)