RPS-BLAST 2.2.22 [Sep-27-2009]

Database: CddB 
           21,608 sequences; 5,994,473 total letters

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

Query= gi|254780812|ref|YP_003065225.1| uroporphyrinogen decarboxylase
[Candidatus Liberibacter asiaticus str. psy62]
         (346 letters)



>gnl|CDD|178875 PRK00115, hemE, uroporphyrinogen decarboxylase; Validated.
          Length = 346

 Score =  441 bits (1136), Expect = e-124
 Identities = 143/343 (41%), Positives = 209/343 (60%), Gaps = 12/343 (3%)

Query: 7   KILEVLQGNVINPPPIWLMRQAGRYLPEYRQIRKKFKNFLDMCYTPEYTVELTLQPIRRY 66
           + L  L+G  ++  P+W+MRQAGRYLPEYR +R K  +FL++C  PE   E+TLQP+RRY
Sbjct: 7   RFLRALRGEPVDRTPVWMMRQAGRYLPEYRALRAKAGSFLELCKNPELAAEVTLQPVRRY 66

Query: 67  NFDAAILFSDILVIADALGRNVRFVENEGPRMD-PITTQE----IYLLNPNIDLFLNYLL 121
             DAAILFSDIL   DA+G ++ F E EGP  D PI T+     + + +P  D     L 
Sbjct: 67  GVDAAILFSDILTPPDAMGLDLDFEEGEGPVFDNPIRTEADVEKLPVPDPEED-----LP 121

Query: 122 PIFQSISILRKKLPNHITLIGFCGAPWTVASYMISGGFIKDHGQNRVFAYQNSRAFNWLL 181
            + +++ +LR++L   + LIGF GAPWT+A+YM+ GG  KD+ + +   Y      + LL
Sbjct: 122 YVLEAVRLLRRELGGEVPLIGFAGAPWTLATYMVEGGGSKDYAKTKAMMYAEPELLHALL 181

Query: 182 DFLSDVSAEYLIAQIHAGVDVIQIFDTHAGCLGEHEFENYAARSVGRIISAVRRKYPNAK 241
           D L+D +  YL AQI AG   +QIFD+ AG L   ++  +    + RI++ ++R++P+  
Sbjct: 182 DKLADATIAYLNAQIEAGAQAVQIFDSWAGALSPADYREFVLPYMKRIVAELKREHPDVP 241

Query: 242 FISFAKGAGYMLKNYRRLTDSNAIGLDWSVPLSFALE-LQKEGPVQGNLDPMRLVVGNQV 300
            I F KGAG +L+     T ++ +GLDW+V L+ A   +  +  +QGNLDP  L+   + 
Sbjct: 242 VILFGKGAGELLEAMAE-TGADVVGLDWTVDLAEARRRVGDKKALQGNLDPAVLLAPPEA 300

Query: 301 MIDGVNAILDVLGSGPFIFNLGHGITPQVDPKNVLDLVKTVRS 343
           + + V AILD  G    IFNLGHGI P+  P+NV  LV+ V  
Sbjct: 301 IEEEVRAILDGGGGPGHIFNLGHGILPETPPENVKALVEAVHE 343


>gnl|CDD|162374 TIGR01464, hemE, uroporphyrinogen decarboxylase.  This model
           represents uroporphyrinogen decarboxylase (HemE), which
           converts uroporphyrinogen III to coproporphyrinogen III.
           This step takes the pathway toward protoporphyrin IX, a
           common precursor of both heme and chlorophyll, rather
           than toward precorrin 2 and its products.
          Length = 338

 Score =  384 bits (988), Expect = e-107
 Identities = 152/342 (44%), Positives = 211/342 (61%), Gaps = 9/342 (2%)

Query: 7   KILEVLQGNVINPPPIWLMRQAGRYLPEYRQIRKKFKNFLDMCYTPEYTVELTLQPIRRY 66
             L   +G  ++ PP+WLMRQAGRYLPEYR++R K  +FL++C  P+  VE+TLQPIRR+
Sbjct: 1   LFLRAAKGEEVDRPPVWLMRQAGRYLPEYRELRAKAPDFLELCRNPDLAVEVTLQPIRRF 60

Query: 67  NFDAAILFSDILVIADALGRNVRFVENEGPRM-DPITTQE--IYLLNPNIDLFLNYLLPI 123
             DAAILFSDILV   ALG +V FVE +GP + +PI T E    L   + +  L Y+   
Sbjct: 61  GVDAAILFSDILVPLQALGLDVDFVEGKGPVIPEPIRTPEDVERLKEFDPESELPYV--- 117

Query: 124 FQSISILRKKLPNHITLIGFCGAPWTVASYMISGGFIKDHGQNRVFAYQNSRAFNWLLDF 183
           +++I +LR++LP  + LIGF GAPWT+ASYMI GG  KD  + + F YQ     + LL+ 
Sbjct: 118 YEAIKLLREELPGEVPLIGFAGAPWTLASYMIEGGGSKDFAKAKRFMYQEPEVLHALLNK 177

Query: 184 LSDVSAEYLIAQIHAGVDVIQIFDTHAGCLGEHEFENYAARSVGRIISAVRRKYPNAKFI 243
           L+D + EYL+ Q+ AG   +QIFD+ AG L   +FE +    + +II  V+ + PN   I
Sbjct: 178 LTDATIEYLVEQVKAGAQAVQIFDSWAGALSPEDFEEFVLPYLKKIIEEVKARLPNVPVI 237

Query: 244 SFAKGAGYMLKNYRRLTDSNAIGLDWSVPLSFA-LELQKEGPVQGNLDPMRLVVGNQVMI 302
            FAKGAG++L+       ++ +GLDW+V L  A   +     +QGNLDP  L    + + 
Sbjct: 238 LFAKGAGHLLEELAETG-ADVVGLDWTVDLKEARKRVGPGVAIQGNLDPAVLYAPEEALE 296

Query: 303 DGVNAILDVL-GSGPFIFNLGHGITPQVDPKNVLDLVKTVRS 343
           + V  IL+   G   +IFNLGHGI P   P+NV  LV+ V S
Sbjct: 297 EKVEKILEAFGGKSRYIFNLGHGILPDTPPENVKALVEYVHS 338


>gnl|CDD|178052 PLN02433, PLN02433, uroporphyrinogen decarboxylase.
          Length = 345

 Score =  281 bits (722), Expect = 2e-76
 Identities = 119/331 (35%), Positives = 186/331 (56%), Gaps = 10/331 (3%)

Query: 20  PPIWLMRQAGRYLPEYRQIRKKFKNFLDMCYTPEYTVELTLQPIRRYNFDAAILFSDILV 79
           PP+WLMRQAGRY+ EYR++ KK+ +F +   TP+  VE++LQP R +  D  ILFSDIL 
Sbjct: 13  PPVWLMRQAGRYMKEYRELCKKYPSFRERSETPDLAVEISLQPWRAFKPDGVILFSDILT 72

Query: 80  IADALGRNVRFVENEGPR-MDPITTQE-IYLLNPNIDLFLNYLLPIFQSISILRKKLPNH 137
              A+G     V+ +GP   +PI ++E +  L+P        L  + +++ ILRK++ N 
Sbjct: 73  PLPAMGIPFDIVKGKGPVIPNPIRSEEDVKRLHPLD--PEEKLPFVGEALKILRKEVGNE 130

Query: 138 ITLIGFCGAPWTVASYMISGGFIKDHGQNRVFAYQNSRAFNWLLDFLSDVSAEYLIAQIH 197
             ++GF GAPWT+A+Y++ GG  K++   +  A+      + LLD L+D   EY+  QI 
Sbjct: 131 AAVLGFVGAPWTLATYIVEGGSSKNYKVIKKMAFTAPEVLHALLDKLTDAVIEYVDYQID 190

Query: 198 AGVDVIQIFDTHAGCLGEHEFENYAARSVGRIISAVRRKYPNAKFISFAKGAGYMLKNYR 257
           AG  V+QIFD+ AG L   +FE ++   + +I+  V+ ++P+   I +A G+G +L+   
Sbjct: 191 AGAQVVQIFDSWAGHLSPVDFEEFSKPYLEKIVDEVKARHPDVPLILYANGSGGLLE--- 247

Query: 258 RLTDSNA--IGLDWSVPLSFALE-LQKEGPVQGNLDPMRLVVGNQVMIDGVNAILDVLGS 314
           RL  +    IGLDW+V ++ A   L  +  VQGN+DP  L    + +   V  ++   G 
Sbjct: 248 RLAGTGVDVIGLDWTVDMADARRRLGSDVAVQGNVDPAVLFGSKEAIEKEVRDVVKKAGP 307

Query: 315 GPFIFNLGHGITPQVDPKNVLDLVKTVRSEK 345
              I NLGHG+      +NV       R  +
Sbjct: 308 QGHILNLGHGVLVGTPEENVAHFFDVARELR 338


>gnl|CDD|180490 PRK06252, PRK06252, methylcobalamin:coenzyme M methyltransferase;
           Validated.
          Length = 339

 Score = 55.7 bits (135), Expect = 2e-08
 Identities = 87/382 (22%), Positives = 143/382 (37%), Gaps = 89/382 (23%)

Query: 5   KQKILEVLQGNVINPPP---------IWLMRQAGRYLPEYRQIRKKFKNFLDMCYTPEYT 55
           K+++L  L+G  ++  P         + LM   G Y PE                 PE  
Sbjct: 6   KERLLNALKGKEVDRVPVICVTQTGTVELMDITGAYWPEAH-------------SDPEKM 52

Query: 56  VELTLQPIRRYNFDAAILFSDILVIADALGRNVRFVENEG-----PRM--DPITTQEIYL 108
            +L +       F+A  +   + V A+A+G  V    + G     P +   PI     Y 
Sbjct: 53  ADLAIAGYEVAGFEAVRVPFCMTVEAEAMGCEV----DMGTKDRQPSVTKYPIKKDVEYR 108

Query: 109 LNPNIDLFLNYLLPIFQSISILRKKLPNHITLIGFCGAPWTVASYMISG--GFIKDHGQN 166
             P+  L    +  + ++I IL++K+   + +I     P ++AS  + G   F+K   + 
Sbjct: 109 KLPDDLLEEGRIPTVLEAIKILKEKVGEEVPIIAGLTGPISLAS-SLMGPKNFLKWLIKK 167

Query: 167 RVFAYQNSRAFNWLLDFLSDVSAEYLIAQIHAGVDVIQIFDTHAG--CLGEHEFENYAAR 224
              A++        LDF++D   EY  AQ+ AG DVI I D  A    LG   FE +   
Sbjct: 168 PELAHE-------FLDFVTDFCIEYAKAQLEAGADVICIADPSASPELLGPKMFEEFVLP 220

Query: 225 SVGRIISAVRRKYPNAKFISFAKGAGYMLKNYRRLTD---------SNAIGLDWSVPLSF 275
            + +II  V             KG   +L     LT           + I +D  V +  
Sbjct: 221 YLNKIIDEV-------------KGLPTILHICGDLTSILEEMADCGFDGISIDEKVDVKT 267

Query: 276 ALE-LQKEGPVQGNLDPMRLV----------VGNQVMIDGVNAILDVLGSGPFIFNLGHG 324
           A E +     + GN+     +             + + DGV    D+L   P     G G
Sbjct: 268 AKENVGDRAALIGNVSTSFTLLNGTPEKVKAEAKKCLEDGV----DIL--AP-----GCG 316

Query: 325 ITPQVDPKNVLDLVKTVRSEKI 346
           I P+   +N+  +V+  +    
Sbjct: 317 IAPKTPLENIKAMVEARKEYYA 338


>gnl|CDD|130530 TIGR01463, mtaA_cmuA, methyltransferase, MtaA/CmuA family.  This
           subfamily is closely related to, yet is distinct from,
           uroporphyrinogen decarboxylase (EC 4.1.1.37). It
           includes two isozymes from Methanosarcina barkeri of
           methylcobalamin--coenzyme M methyltransferase. It also
           includes a chloromethane utilization protein, CmuA,
           which transfers the methyl group of chloromethane to a
           corrinoid protein.
          Length = 340

 Score = 49.5 bits (118), Expect = 1e-06
 Identities = 46/195 (23%), Positives = 73/195 (37%), Gaps = 32/195 (16%)

Query: 24  LMRQAGRYLPEYRQIRKKFKNFLDMCYTPEYTVELTLQPIRRYNFDAAILFSDILVIADA 83
           LMR+ G   PE                  E    L +    ++  +A     D+   A+ 
Sbjct: 34  LMRECGATWPEAH-------------RDGEAMAHLAIAAYEKFGGEAVRPPFDLTTEAEC 80

Query: 84  LGRNVRFVENEGPRMDPITTQEIYLLNP-NIDLFLNYLLP------IFQSISILRKKLPN 136
           +G  +    + GP   P  T+     N  +     NYLL       + ++I ILR++  +
Sbjct: 81  VGCEL----DYGPYAQPSVTKHPTPTNLADYRYPENYLLKPGRIPVVLEAIKILRERYGD 136

Query: 137 HITLIGFCGAPWTVASYMISG-GFIKDHGQNRVFAYQNSRAFNWLLDFLSDVSAEYLIAQ 195
              +IG  G P+T+A  MI    F+        +   +      +L+   D    Y  A 
Sbjct: 137 THPIIGPMGGPFTLAQLMIGVSEFLS-------WISTDPDYAKAVLELALDFVIAYAKAM 189

Query: 196 IHAGVDVIQIFDTHA 210
           + AG DVI I D  A
Sbjct: 190 VEAGADVIAIADPFA 204


>gnl|CDD|163134 TIGR03098, ligase_PEP_1, acyl-CoA ligase (AMP-forming), exosortase
           system type 1 associated.  This group of proteins
           contains an AMP-binding domain (pfam00501) associated
           with acyl CoA-ligases. These proteins are generally
           found in genomes containing the exosortase/PEP-CTERM
           protein expoert system, specifically the type 1 variant
           of this system described by the Genome Property
           GenProp0652. When found in this context they are
           invariably present next to a decarboxylase enzyme. A
           number of sequences from Burkholderia species also hit
           this model, but the genomic context is obviously
           different. The hypothesis of a constant substrate for
           this family is only strong where the exosortase context
           is present.
          Length = 515

 Score = 29.0 bits (65), Expect = 1.8
 Identities = 13/44 (29%), Positives = 20/44 (45%)

Query: 78  LVIADALGRNVRFVENEGPRMDPITTQEIYLLNPNIDLFLNYLL 121
           L   ++   ++R++ N G  M   T   +    PN  LFL Y L
Sbjct: 266 LDWPESAAPSLRYLTNSGGAMPRATLSRLRSFLPNARLFLMYGL 309


>gnl|CDD|181678 PRK09177, PRK09177, xanthine-guanine phosphoribosyltransferase;
           Validated.
          Length = 156

 Score = 28.3 bits (64), Expect = 2.9
 Identities = 12/25 (48%), Positives = 14/25 (56%), Gaps = 1/25 (4%)

Query: 227 GRIISAVRRKYPNAKFIS-FAKGAG 250
           G    AVR  YP A F + +AK AG
Sbjct: 97  GGTARAVREMYPKAHFATVYAKPAG 121


>gnl|CDD|178627 PLN03078, PLN03078, Putative tRNA pseudouridine synthase;
           Provisional.
          Length = 513

 Score = 27.9 bits (62), Expect = 3.6
 Identities = 15/39 (38%), Positives = 17/39 (43%)

Query: 214 GEHEFENYAARSVGRIISAVRRKYPNAKFISFAKGAGYM 252
           GEH F NY ARS  R     + K  N      AK +  M
Sbjct: 234 GEHPFHNYTARSKYRKKLPGKHKQRNGAVSRRAKSSKEM 272


>gnl|CDD|184142 PRK13558, PRK13558, bacterio-opsin activator; Provisional.
          Length = 665

 Score = 27.9 bits (62), Expect = 4.1
 Identities = 8/25 (32%), Positives = 13/25 (52%), Gaps = 2/25 (8%)

Query: 82  DALGRNVRFVENEGPRMDPITTQEI 106
           + LGRN RF+  +G   +     E+
Sbjct: 190 EVLGRNCRFL--QGEDTNEERVAEL 212


>gnl|CDD|130457 TIGR01390, CycNucDiestase, 2',3'-cyclic-nucleotide
           2'-phosphodiesterase.  2',3'-cyclic-nucleotide
           2'-phosphodiesterase is a bifunctional enzyme localized
           to the periplasm of Gram-negative bacteria.
           2',3'-cyclic-nucleotide 2'-phosphodiesters are
           intermediates formed during the hydrolysis of RNA by the
           ribonuclease I, which is also found to the periplasm,
           and other enzymes of the RNAse T2 family. Bacteria are
           unable to transport 2',3'-cyclic-nucleotides into the
           cytoplasm. 2',3'-cyclic-nucleotide 2'-phosphodiesterase
           contains 2 active sites which catalyze the reactions
           that convert the 2',3'-cyclic-nucleotide into a
           3'-nucleotide, which is then converted into nucleic acid
           and phosphate. Both final products can be transported
           into the cytoplasm. Thus, it has been suggested that
           2',3'-cyclic-nucleotide 2'-phosphodiesterase has a
           'scavenging' function. Experimental evidence indicates
           that 2',3'-cyclic-nucleotide 2'-phosphodiesterase
           enables Yersinia enterocolitica O:8 to grow on 2'3'-cAMP
           as a sole source of carbon and energy (PubMed:11160814).
          Length = 626

 Score = 27.5 bits (61), Expect = 5.3
 Identities = 14/49 (28%), Positives = 22/49 (44%), Gaps = 1/49 (2%)

Query: 195 QIHAGVDVIQIFDTHAGCLGEHEFENYAARSVGRIISAVRRKYPNAKFI 243
           Q+H     + +     G LG HEF NY    + + I+A +    NA  +
Sbjct: 75  QMHPVYKAMNLLKYDVGNLGNHEF-NYGLPFLKQAIAAAKFPIVNANVV 122


>gnl|CDD|152330 pfam11894, DUF3414, Protein of unknown function (DUF3414).  This
            family of proteins are functionally uncharacterized. This
            protein is found in eukaryotes. Proteins in this family
            are typically between 764 to 2011 amino acids in length.
            This protein has a conserved LLG sequence motif.
          Length = 1611

 Score = 27.3 bits (61), Expect = 6.1
 Identities = 24/124 (19%), Positives = 42/124 (33%), Gaps = 22/124 (17%)

Query: 6    QKILEVLQGNVINPPPIWLMRQAGRYLPEYRQIRKKFKNFLDMCYTPEYTVELTLQPIRR 65
            +K L+ + G  I+  P  L   A             ++    +C  P  T   TL+ +R 
Sbjct: 991  EKSLDSISGLNIDEAPPRLAELA-------------YQLLQKLCSNP-LTSGPTLRYLRS 1036

Query: 66   YNFDAAILFSDILVIADALGRNVRFVENEGPRMDPITTQEIYLLNPNIDLFLNYLLPIFQ 125
             +F    L S   +  + L   + F  +    +       I         FLN    + Q
Sbjct: 1037 NDFLFRHLASLPFIDPNTLWDGLSFAADNKFFLSSSIGALIS--------FLNQRSWLLQ 1088

Query: 126  SISI 129
             ++I
Sbjct: 1089 YLAI 1092


>gnl|CDD|184632 PRK14336, PRK14336, (dimethylallyl)adenosine tRNA
           methylthiotransferase; Provisional.
          Length = 418

 Score = 26.8 bits (59), Expect = 7.8
 Identities = 11/27 (40%), Positives = 17/27 (62%), Gaps = 3/27 (11%)

Query: 226 VGRIISAVRRKYPNAKFISFAKGAGYM 252
           VG+ IS +R+K+P   F+ +  G G M
Sbjct: 83  VGQDISLIRKKFP---FVDYIFGPGSM 106


>gnl|CDD|178282 PLN02678, PLN02678, seryl-tRNA synthetase.
          Length = 448

 Score = 26.6 bits (59), Expect = 9.3
 Identities = 16/60 (26%), Positives = 23/60 (38%), Gaps = 8/60 (13%)

Query: 130 LRKKLPNHITLIGFCGAPWTVASYMISGG---FIKDHGQNRVFAYQNSRAFNWLLDFLSD 186
              KL NH+ L+   G   T     ++GG   ++K  G        N    N+ L FL  
Sbjct: 136 QEPKLKNHVDLVELLGIVDTERGADVAGGRGYYLKGAG-----VLLNQALINFGLAFLRK 190


>gnl|CDD|180592 PRK06498, PRK06498, isocitrate lyase; Provisional.
          Length = 531

 Score = 26.5 bits (59), Expect = 9.6
 Identities = 10/24 (41%), Positives = 14/24 (58%)

Query: 160 IKDHGQNRVFAYQNSRAFNWLLDF 183
           I++   N    Y NS +FNW L+F
Sbjct: 368 IREVVPNAKLVYNNSPSFNWTLNF 391


  Database: CddB
    Posted date:  Feb 4, 2011  9:54 PM
  Number of letters in database: 5,994,473
  Number of sequences in database:  21,608
  
Lambda     K      H
   0.324    0.142    0.428 

Gapped
Lambda     K      H
   0.267   0.0744    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 5,968,528
Number of extensions: 400947
Number of successful extensions: 837
Number of sequences better than 10.0: 1
Number of HSP's gapped: 824
Number of HSP's successfully gapped: 25
Length of query: 346
Length of database: 5,994,473
Length adjustment: 94
Effective length of query: 252
Effective length of database: 3,963,321
Effective search space: 998756892
Effective search space used: 998756892
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: 41 (22.0 bits)
S2: 58 (26.1 bits)