RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|255764510|ref|YP_003065448.2| uroporphyrinogen-III synthase
[Candidatus Liberibacter asiaticus str. psy62]
         (232 letters)



>3mw8_A Uroporphyrinogen-III synthase; structural genomics, joint center
           for structural genomics, J protein structure initiative,
           PSI-2, lyase; 1.65A {Shewanella amazonensis}
          Length = 240

 Score = 86.4 bits (213), Expect = 6e-18
 Identities = 33/240 (13%), Positives = 73/240 (30%), Gaps = 11/240 (4%)

Query: 1   MYIVITRPIKKALRTQEKIQKMGYIPVMMPLSYFIHDRES-VFLAMQQSYGAIAITSSES 59
           M +++TRP  K       +  +    ++ PL        +   L        +   S+ +
Sbjct: 2   MKLLLTRPEGKNAAMASALDALAIPYLVEPLLSVEAAAVTQAQLDELSRADILIFISTSA 61

Query: 60  LSTLPANFCR---HTPIFAIGEASACLARQKGFTQIFHGKDNSINLAKIIVEQKVLFTPQ 116
           +S               +A+G+A+A     +G T      D+      + +      + +
Sbjct: 62  VSFATPWLKDQWPKATYYAVGDATADALALQGITAERSPADSQATEGLLTLPSLEQVSGK 121

Query: 117 KPLIYLGGKPRNFHFEDYLIEHKIPLRVIDCYYSQDIAYPETTMKNLLQNA--DAILFYA 174
           + +I  G   R     D L      +  ++ Y             +  Q+   D I+  +
Sbjct: 122 QIVIVRGKGGREAM-ADGLRLRGANVSYLEVYQRACPPLDAPASVSRWQSFGIDTIVVTS 180

Query: 175 RSSVLYFFSL----PLPAKISAAFLCLSNNIASAIPASYKNVVTVACFPKETSLLKLLPL 230
              +    +L              +  S  + +         VT A    + ++L  L +
Sbjct: 181 GEVLENLINLVPKDSFAWLRDCHIIVPSARVETQARKKGLRRVTNAGAANQAAVLDALGM 240


>1jr2_A Uroporphyrinogen-III synthase; heme biosynthesis, HEAM
           biosynthesis, lyase; 1.84A {Homo sapiens} SCOP:
           c.113.1.1
          Length = 286

 Score = 72.5 bits (177), Expect = 8e-14
 Identities = 36/255 (14%), Positives = 77/255 (30%), Gaps = 32/255 (12%)

Query: 3   IVITRPIKKAL---RTQEKIQKMGYIPVMMPL---SYFIHDRESVFLAMQQSYGAIAITS 56
           +++    +          ++   G    ++P+    +      S  L+  + YG +  TS
Sbjct: 25  LLLKDAKEDDCGQDPYIRELGLYGLEATLIPVLSFEFLSLPSFSEKLSHPEDYGGLIFTS 84

Query: 57  SESLSTL----------------PANFCRHTPIFAIGEASACLARQKGFTQIFHGKDNSI 100
             ++                            ++ +G A+A L  + G         N+ 
Sbjct: 85  PRAVEAAELCLEQNNKTEVWERSLKEKWNAKSVYVVGNATASLVSKIGLDTEGETCGNAE 144

Query: 101 NLAKIIVEQKVLFTPQKPLIYLGGKPRNFHFEDYLIEHKIPLRVIDCYYSQDIAYPETTM 160
            LA+ I  ++       PL++  G  +       L +  I +  I  Y +      +  +
Sbjct: 145 KLAEYICSRES---SALPLLFPCGNLKREILPKALKDKGIAMESITVYQTVAHPGIQGNL 201

Query: 161 KNLLQNA---DAILFYARSSVLYFFSL----PLPAKISAAFLCLSNNIASAIPASYKNVV 213
            +         +I F++ S + Y                 F  +    A A+ A    V 
Sbjct: 202 NSYYSQQGVPASITFFSPSGLTYSLKHIQELSGDNIDQIKFAAIGPTTARALAAQGLPVS 261

Query: 214 TVACFPKETSLLKLL 228
             A  P   +L   +
Sbjct: 262 CTAESPTPQALATGI 276


>3p9z_A Uroporphyrinogen III cosynthase (HEMD); MCSG, PSI2, structural
           genomics, protein structure initiativ midwest center for
           structural genomics; HET: MSE; 2.10A {Helicobacter
           pylori}
          Length = 229

 Score = 59.7 bits (144), Expect = 6e-10
 Identities = 32/190 (16%), Positives = 64/190 (33%), Gaps = 14/190 (7%)

Query: 48  SYGAIAITSSES--------LSTLPANFCRHTPIFAIGEASACLARQKGFTQIFHGKDNS 99
            + A+  TS  +         ++      ++ P +A+ E +A   +   F   F G+   
Sbjct: 37  PFNALIFTSKNAVFSLLETLKNSPKLKMLQNIPAYALSEPTAKTLQDHHFKVAFMGEKAH 96

Query: 100 INLAKIIVEQKVLFTPQKPLIYLGGKPRNFHFEDYLIEHKIPLRVIDCYYSQDIAYPETT 159
               K  V++      +K ++YL  K      +  L+EH I  +    Y ++      + 
Sbjct: 97  ---GKEFVQEIFPLLEKKSVLYLRAKEIVSSLDTILLEHGIDFKQAVVYENKLKHLTLSE 153

Query: 160 MKNLLQN-ADAILFYARSSVLYFFSLPLPAKISAAFLCLSNNIASAIPASYKNVVTVACF 218
              L       ++F A S    F         +   + + N  A  +         +A  
Sbjct: 154 QNALKPKEKSILIFTAISHAKAFLHY-FEFLENYTAISIGNTTALYLQEQGIPSY-IAKK 211

Query: 219 PKETSLLKLL 228
           P   + L+L 
Sbjct: 212 PSLEACLELA 221


>1wcw_A Uroporphyrinogen III synthase; congenital erythropoietic porphyria,
           structural genomics, riken structural
           genomics/proteomics initiative; 1.30A {Thermus
           thermophilus} PDB: 1wd7_A 1wcx_A
          Length = 261

 Score = 50.4 bits (120), Expect = 3e-07
 Identities = 34/244 (13%), Positives = 70/244 (28%), Gaps = 27/244 (11%)

Query: 1   MYIVITRPIKKALRTQEKIQKMGYIPVMMPLSYF----IHDRESVFLAMQQSYGAIAITS 56
           + +      ++    +   +K+G+ P++ P+       + +      A+ Q       T+
Sbjct: 9   VRVAYAGL-RRKEAFKALAEKLGFTPLLFPVQATEKVPVPEYRDQVRALAQGVDLFLATT 67

Query: 57  SESLSTL----------PANFCRHTPIFAIGEASACLARQKGFTQIFHGKDNSINLAKII 106
              +  L                     A G  +A   ++ G      G   S +L  ++
Sbjct: 68  GVGVRDLLEAGKALGLDLEGPLAKAFRLARGAKAARALKEAGLPPHAVGDGTSKSLLPLL 127

Query: 107 VEQKVLFTPQKPLIYLGGKPRNFHFEDYLIEHKIPLRVIDCYYSQDIAYPETTMKNLLQN 166
            + +         + L GKP     E+ L E    +  +  Y           ++  L  
Sbjct: 128 PQGR-----GVAALQLYGKPLPL-LENALAERGYRVLPLMPYRHLPDPEGILRLEEALLR 181

Query: 167 A--DAILFYARSSVLYFFSLPLPAKISAAFLCLSNNIASAIPASYKNV----VTVACFPK 220
              DA+ F A   V + F      K     L       +    +   +    V      +
Sbjct: 182 GEVDALAFVAAIQVEFLFEGAKDPKALREALNTRVKALAVGRVTADALREWGVKPFYVDE 241

Query: 221 ETSL 224
              L
Sbjct: 242 TERL 245


>3d8t_A Uroporphyrinogen-III synthase; heme biosynthesis, lyase; 1.60A
           {Thermus thermophilus} PDB: 3d8r_A 3d8s_A 3d8n_A
          Length = 286

 Score = 48.1 bits (114), Expect = 2e-06
 Identities = 36/244 (14%), Positives = 67/244 (27%), Gaps = 27/244 (11%)

Query: 1   MYIVITRPIKKALRTQEKIQKMGYIPVMMPLS--YFIHDRESVFLAMQ--QSYGAIAITS 56
           M I      ++    +   +K+G+ P++ P+     +   E      +  Q       T+
Sbjct: 34  MRIAYAGL-RRKEEFKALAEKLGFTPLLFPVQATEKVPVPEYRDQVRELAQGVDLFLATT 92

Query: 57  SESLSTLPANFCRH----------TPIFAIGEASACLARQKGFTQIFHGKDNSINLAKII 106
              +  L                     A G  +A   ++ G      G   S +L  ++
Sbjct: 93  GVGVRDLLEAGKALGLDLEGPLAKAFRLARGAKAARALKEAGLPPHAVGDGTSKSLLPLL 152

Query: 107 VEQKVLFTPQKPLIYLGGKPRNFHFEDYLIEHKIPLRVIDCYYSQDIAYP--ETTMKNLL 164
            + +         + L GKP     E+ L E    +  +  Y                L 
Sbjct: 153 PQGR-----GVAALQLYGKPLPL-LENALAERGYRVLPLMPYRHLPDPEGILRLEEAVLR 206

Query: 165 QNADAILFYARSSVLYFFSLPLPAKISAAFLCLSNNIASAIPASYKNV----VTVACFPK 220
              DA+ F A   V + F      K     L       +    +   +    V      +
Sbjct: 207 GEVDALAFVAAIQVEFLFEGAKDPKALREALNTRVKALAVGRVTADALREWGVKPFYVDE 266

Query: 221 ETSL 224
              L
Sbjct: 267 TERL 270


>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 = 33.8 bits (77), Expect = 0.031
 Identities = 44/271 (16%), Positives = 76/271 (28%), Gaps = 105/271 (38%)

Query: 9   IKKALRTQEKIQKMGY---IPVMMPL-------SYFI-------HDRESVFLAMQQ---- 47
           I + L          Y   IP+  PL        Y +          E     ++     
Sbjct: 215 ILEWLENPSNTPDKDYLLSIPISCPLIGVIQLAHYVVTAKLLGFTPGE-----LRSYLKG 269

Query: 48  ----SYG---AIAITSSESLSTLPANFCRHTPI---FAIGEASACLARQKGFTQIFHGKD 97
               S G   A+AI  ++S  +   +      I   F IG         + +        
Sbjct: 270 ATGHSQGLVTAVAIAETDSWESFFVSV--RKAITVLFFIGVRC-----YEAYPNTS---- 318

Query: 98  NSINLAKIIVEQKV---LFTPQKPLIYLGGKPRNFHFEDYLIEHKIPLRVID---CYYSQ 151
               L   I+E  +      P  P++ +    +     + + ++      ++    +   
Sbjct: 319 ----LPPSILEDSLENNEGVPS-PMLSISNLTQ-----EQVQDY------VNKTNSHLPA 362

Query: 152 D----IAYPETTMKNLLQNADAILFYARSSV-------LYFFSLPLPAKISAAFLCLSNN 200
                I+         L N       A++ V       LY  +L L  K  A     S  
Sbjct: 363 GKQVEIS---------LVNG------AKNLVVSGPPQSLYGLNLTL-RKAKAP----SGL 402

Query: 201 IASAIPASYKNVVTVACF-----PKETSLLK 226
             S IP S + +     F     P  + LL 
Sbjct: 403 DQSRIPFSERKLKFSNRFLPVASPFHSHLLV 433



 Score = 31.5 bits (71), Expect = 0.16
 Identities = 31/208 (14%), Positives = 56/208 (26%), Gaps = 63/208 (30%)

Query: 48  SYGAIAIT------SSESLSTLPANFCRH----TPIFAIGEASAC----LARQKGFTQIF 93
           S+G++         S    S L   F +     T  FA  +        + +  G+    
Sbjct: 12  SHGSLEHVLLVPTASFFIASQLQEQFNKILPEPTEGFAADDEPTTPAELVGKFLGYV-SS 70

Query: 94  HGKDNSINLAKIIVEQKVL--FTPQKPLIYLGGKPRNFH--FEDYLIEHKIPL----RVI 145
             + + +     ++    L  F       YL G   + H      L E+   L     +I
Sbjct: 71  LVEPSKVGQFDQVL-NLCLTEFENC----YLEGN--DIHALAAKLLQENDTTLVKTKELI 123

Query: 146 DCYY-----SQDIAYPETTMKNLLQNA---DAILFYARSSVL--------YFFSL----- 184
             Y      ++   + + +   L +     +A L  A   +         YF  L     
Sbjct: 124 KNYITARIMAKR-PFDKKSNSALFRAVGEGNAQL-VA---IFGGQGNTDDYFEELRDLYQ 178

Query: 185 -------PLPAKISAAFLCLSNNIASAI 205
                   L    +     L      A 
Sbjct: 179 TYHVLVGDLIKFSAETLSELIRTTLDAE 206


>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 = 29.0 bits (64), Expect = 0.86
 Identities = 38/183 (20%), Positives = 69/183 (37%), Gaps = 33/183 (18%)

Query: 38   RESVFLAMQQSYGAIAITSSESLSTLPANFCRHTPIFAIGEASACLARQKGFTQIFHGKD 97
            +ES    M      + I+SS  + T P   C          A++  +   G   I  GK 
Sbjct: 1077 QESFINTMSAWVNMLLISSSGPIKT-PVGAC----------ATSVESVDIGVETILSGK- 1124

Query: 98   NSINLAKI-IVEQKVLFTPQKPLIYLGGKPRNFHFEDYLIEH-KIPLRVIDCYYSQDIAY 155
                 A+I IV     F  +    +   K  +   E++  EH + P          +++ 
Sbjct: 1125 -----ARICIVGGYDDFQEEGSFEFGNMKATSNTLEEF--EHGRTP---------AEMSR 1168

Query: 156  PETTMKNLLQNADA--ILFYARSSVLYFFSLPLPAKISAAFLCLSNNIASAIPASYKNVV 213
            P TT +N    A    I    ++ +     +P+   ++ A    ++ I  ++PA  K ++
Sbjct: 1169 PATTTRNGFMEAQGAGIQIIMQADLALKMGVPIYGIVAMA-ATATDKIGRSVPAPGKGIL 1227

Query: 214  TVA 216
            T A
Sbjct: 1228 TTA 1230


>2a6h_C DNA-directed RNA polymerase beta chain; RNA polymerase holoenzyme,
           streptolydigin, antibiotic, transcription regulation;
           HET: STD; 2.40A {Thermus thermophilus} SCOP: e.29.1.1
           PDB: 1smy_C* 1zyr_C* 1iw7_C* 2a69_C* 2a6e_C 2a68_C*
           2be5_C* 2cw0_C 2o5i_C 2o5j_C* 2ppb_C* 3dxj_C* 3eql_C*
           1ynj_C* 1ynn_C* 2gho_C 1hqm_C 1l9u_C 1l9z_C 1i6v_C*
          Length = 1119

 Score = 27.8 bits (61), Expect = 2.4
 Identities = 9/35 (25%), Positives = 15/35 (42%)

Query: 1   MYIVITRPIKKALRTQEKIQKMGYIPVMMPLSYFI 35
           +Y  +    K     +E    +G+IP+M     FI
Sbjct: 94  LYARLQLIHKDTGLIKEDEVFLGHIPLMTEDGSFI 128


>1ivz_A Hypothetical protein 1110008I14RIK; structural genomics, SEA
           domain, mucin 16, riken structural genomics/proteomics
           initiative, RSGI; NMR {Mus musculus} SCOP: d.58.41.1
          Length = 132

 Score = 26.3 bits (57), Expect = 6.2
 Identities = 22/56 (39%), Positives = 26/56 (46%), Gaps = 9/56 (16%)

Query: 149 YSQDIAYPETT----MKNLLQNADAILFYARSSVLYFFSLPLPAKISAAFLCLSNN 200
           YSQDIA P TT     K  ++NA   LF   S   YF    +      AF  +SNN
Sbjct: 25  YSQDIAQPSTTKYQQTKRSIENALNQLFRNSSIKSYFSDCQV-----LAFRSVSNN 75


>1tzf_A Glucose-1-phosphate cytidylyltransferase; nucleotidyltransferase,
           mixed alpha/beta fold; HET: C5G; 2.10A {Salmonella
           enterica subsp} SCOP: c.68.1.13 PDB: 1wvc_A*
          Length = 259

 Score = 25.8 bits (55), Expect = 8.2
 Identities = 12/33 (36%), Positives = 17/33 (51%)

Query: 117 KPLIYLGGKPRNFHFEDYLIEHKIPLRVIDCYY 149
           KP++ +GGKP  +H       H I   +I C Y
Sbjct: 25  KPMVEIGGKPILWHIMKMYSVHGIKDFIICCGY 57


  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
   0.325    0.138    0.405 

Gapped
Lambda     K      H
   0.267   0.0530    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 1,874,483
Number of extensions: 79832
Number of successful extensions: 328
Number of sequences better than 10.0: 1
Number of HSP's gapped: 316
Number of HSP's successfully gapped: 15
Length of query: 232
Length of database: 5,693,230
Length adjustment: 89
Effective length of query: 143
Effective length of database: 3,535,514
Effective search space: 505578502
Effective search space used: 505578502
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 55 (25.4 bits)