RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254781037|ref|YP_003065450.1| porphobilinogen deaminase
[Candidatus Liberibacter asiaticus str. psy62]
         (307 letters)



>gnl|CDD|30530 COG0181, HemC, Porphobilinogen deaminase [Coenzyme metabolism].
          Length = 307

 Score =  321 bits (825), Expect = 1e-88
 Identities = 129/296 (43%), Positives = 179/296 (60%), Gaps = 3/296 (1%)

Query: 3   KKPFRIGTRCSPLALAHAFETRSSLMDVHKIPPHNIVIIPLSTKGDRITNRTLTEIGGKG 62
               RIGTR S LALA A E    L   +  P   + I+ + TKGDRI ++ L++IGGKG
Sbjct: 1   MMKLRIGTRGSKLALAQANEVIERLKAAY--PDLEVEIVTIKTKGDRILDKPLSKIGGKG 58

Query: 63  LFTEEIEKKLISGEIDCAVHSAKDMPTKLLKGLQISAYLPREDIRDVFISHTAQSLKDLA 122
           LFT+E+E+ L+ GEID AVHS KD+PT+L +GL ++A   RED RD  +S     L++L 
Sbjct: 59  LFTKELEQALLEGEIDIAVHSLKDVPTELPEGLVLAAIPEREDPRDALVSRDGYDLEELP 118

Query: 123 LHSVIGTSSLRRKALLLRWRSDISVIDFRGKIETRLNKLNNNKAHAILLAYAGIKRLKKE 182
             +V+GTSSLRR+A L   R D+ +   RG ++TRL KL+  +  AI+LA AG+KRL  E
Sbjct: 119 EGAVVGTSSLRRQAQLKALRPDLKIEPLRGNVDTRLRKLDEGEYDAIILAAAGLKRLGLE 178

Query: 183 KVIKEILNIEDFPPSPGQGAICIETHVNNPKAQELVKVINHEDTWDSVNCERAFLAELDG 242
             I EIL+ E+F P+PGQGA+ IE    + K  EL+  +N EDT   V  ERAFL EL+G
Sbjct: 179 NRITEILDPEEFLPAPGQGALAIECRAGDEKVLELLAELNDEDTRICVTAERAFLRELEG 238

Query: 243 SCKSAIAGFA-YCKGSTLYFYGIVLASDGKIFHEVSRNGNRCDAINIGRDAAQYIR 297
            C+  I  +A    G  L    +V + DG    +    G+  DA  +G++ A+ + 
Sbjct: 239 GCQVPIGAYAELTGGGELRLRALVGSPDGSQIIKAEIRGDAEDAEELGKELAEELL 294


>gnl|CDD|29604 cd00494, HMBS, Hydroxymethylbilane synthase (HMBS), also known as
           porphobilinogen deaminase (PBGD), is an intermediate
           enzyme in the biosynthetic pathway of tetrapyrrolic ring
           systems, such as heme, chlorophylls, and vitamin B12.
           HMBS catalyzes the conversion of porphobilinogen (PBG)
           into hydroxymethylbilane (HMB).  HMBS consists of three
           domains, and is believed to bind substrate through a
           hinge-bending motion of domains I and II.  HMBS is found
           in all organisms except viruses..
          Length = 292

 Score =  281 bits (721), Expect = 1e-76
 Identities = 127/289 (43%), Positives = 173/289 (59%), Gaps = 3/289 (1%)

Query: 6   FRIGTRCSPLALAHAFETRSSLMDVHKIPPHNIVIIPLSTKGDRITNRTLTEIGGKGLFT 65
            RIGTR S LAL    +    L ++   P   + I+ + T GD+I ++ L +IGGKGLFT
Sbjct: 1   IRIGTRKSKLALIQTNKVIEKLKELC--PGIEVEIVIIKTTGDKILDKPLAKIGGKGLFT 58

Query: 66  EEIEKKLISGEIDCAVHSAKDMPTKLLKGLQISAYLPREDIRDVFISHTAQSLKDLALHS 125
           +E+E+ L++GEID AVHS KD+PT+L +GL + A   RED RD  +S    SL+DL   S
Sbjct: 59  KELEEALLNGEIDLAVHSLKDVPTELPEGLVLGAIPKREDPRDALVSRNGSSLEDLPAGS 118

Query: 126 VIGTSSLRRKALLLRWRSDISVIDFRGKIETRLNKLNNNKAHAILLAYAGIKRLKKEKVI 185
           V+GTSSLRR+A L R R D+     RG ++TRL KL+  +  AI+LA AG+KRL  E  I
Sbjct: 119 VVGTSSLRRQAQLKRKRPDLKFEPLRGNVDTRLRKLDEGEYDAIILAAAGLKRLGLEDRI 178

Query: 186 KEILNIEDFPPSPGQGAICIETHVNNPKAQELVKVINHEDTWDSVNCERAFLAELDGSCK 245
            + L+ E   P+ GQGA+ IE    + +   L+K +NHE+T   V  ERAFL EL+G C+
Sbjct: 179 TQYLSPEVMLPAVGQGALAIECRKGDEELLALLKPLNHEETALCVLAERAFLRELEGGCQ 238

Query: 246 SAIAGFA-YCKGSTLYFYGIVLASDGKIFHEVSRNGNRCDAINIGRDAA 293
             I  +A    G  L   G+V + DGK   E    GN  DA  +G+  A
Sbjct: 239 VPIGVYAELDGGEELKLKGLVGSPDGKRLIEGEVRGNIEDAEELGKKLA 287


>gnl|CDD|144826 pfam01379, Porphobil_deam, Porphobilinogen deaminase, dipyromethane
           cofactor binding domain. 
          Length = 213

 Score =  230 bits (588), Expect = 4e-61
 Identities = 98/214 (45%), Positives = 133/214 (62%), Gaps = 2/214 (0%)

Query: 6   FRIGTRCSPLALAHAFETRSSLMDVHKIPPHNIVIIPLSTKGDRITNRTLTEIGGKGLFT 65
            RIGTR S LAL         L ++   P   + I+ + T GD+I ++ L +IGGKGLFT
Sbjct: 2   IRIGTRKSKLALIQTNHVIEKLKELC--PDIEVEIVIIKTTGDKILDKPLAKIGGKGLFT 59

Query: 66  EEIEKKLISGEIDCAVHSAKDMPTKLLKGLQISAYLPREDIRDVFISHTAQSLKDLALHS 125
           +E+E+ L++GEID AVHS KD+PT+L +GL + A   RED RD  +S   +SL+DL   S
Sbjct: 60  KELEEALLNGEIDLAVHSLKDVPTELPEGLVLGAIPKREDPRDALVSRNGKSLEDLPEGS 119

Query: 126 VIGTSSLRRKALLLRWRSDISVIDFRGKIETRLNKLNNNKAHAILLAYAGIKRLKKEKVI 185
           V+GTSSLRR A L R R D+     RG ++TRL KL+  +  AI+LA AG+KRL  E  I
Sbjct: 120 VVGTSSLRRSAQLKRKRPDLKFEPLRGNVDTRLRKLDEGEYDAIILAAAGLKRLGLEDRI 179

Query: 186 KEILNIEDFPPSPGQGAICIETHVNNPKAQELVK 219
            + L  ED  P+ GQGA+ IE    + +   L+K
Sbjct: 180 TQSLPPEDMLPAVGQGALAIECRKGDEEILALLK 213


>gnl|CDD|38103 KOG2892, KOG2892, KOG2892, Porphobilinogen deaminase [Coenzyme
           transport and metabolism].
          Length = 320

 Score =  224 bits (572), Expect = 3e-59
 Identities = 114/284 (40%), Positives = 160/284 (56%), Gaps = 6/284 (2%)

Query: 1   MEKKPFRIGTRCSPLALAHAFETRSSLMDVHKIPPHNIVIIPLSTKGDRITNRTLTEIGG 60
                 RIGTR S LA+  ++  R  L   +  P     II +ST GD+I ++ L +IGG
Sbjct: 3   PRTAVIRIGTRKSKLAVIQSYHVREKLEKKY--PELAFEIITMSTTGDKILSKPLAKIGG 60

Query: 61  KGLFTEEIEKKLISGEIDCAVHSAKDMPTKLLKGLQISAYLPREDIRDVFISHT---AQS 117
           K LFT+E+E  LI+G +D  VHS KD+PT L +G+ I   L RED RD  +  T    ++
Sbjct: 61  KSLFTKELEDALINGHVDIVVHSLKDLPTYLPEGMIIGCILKREDPRDALVFLTYSAYKT 120

Query: 118 LKDLALHSVIGTSSLRRKALLLRWRSDISVIDFRGKIETRLNKLNNNKA-HAILLAYAGI 176
           L DL   SV+GTSSLRRKA +LR    + V   RG ++TRL+KL+  K   AI+LA AG+
Sbjct: 121 LADLPAGSVVGTSSLRRKAQILRKYPHLHVESIRGNLQTRLSKLDGGKPFQAIILALAGL 180

Query: 177 KRLKKEKVIKEILNIEDFPPSPGQGAICIETHVNNPKAQELVKVINHEDTWDSVNCERAF 236
           KR+     I +IL+ ++   + GQGA+ IE   ++ K    +  +N  +T   +  ERAF
Sbjct: 181 KRMGWTNRIAQILHPDEMLYAVGQGALGIECRADDDKMLTYLASLNDLNTTLRILAERAF 240

Query: 237 LAELDGSCKSAIAGFAYCKGSTLYFYGIVLASDGKIFHEVSRNG 280
           L  L+G C   IA ++  K   L   G+V + DG    E SR G
Sbjct: 241 LRTLEGGCSVPIAVYSSKKEGNLILTGLVWSLDGTKVIETSRKG 284


>gnl|CDD|146500 pfam03900, Porphobil_deamC, Porphobilinogen deaminase, C-terminal
           domain. 
          Length = 74

 Score = 64.6 bits (158), Expect = 3e-11
 Identities = 24/67 (35%), Positives = 33/67 (49%)

Query: 227 WDSVNCERAFLAELDGSCKSAIAGFAYCKGSTLYFYGIVLASDGKIFHEVSRNGNRCDAI 286
              V  ERAFL EL+G C+  I  +A  K   L   G+V + DG    E+   G+  DA 
Sbjct: 1   ALCVLAERAFLRELEGGCQVPIGAYAVLKDGNLRLKGLVGSPDGTRVFEIEVRGDIEDAE 60

Query: 287 NIGRDAA 293
            +G+  A
Sbjct: 61  ELGKKLA 67


>gnl|CDD|30363 COG0013, AlaS, Alanyl-tRNA synthetase [Translation, ribosomal
           structure and biogenesis].
          Length = 879

 Score = 28.7 bits (64), Expect = 2.0
 Identities = 41/162 (25%), Positives = 65/162 (40%), Gaps = 25/162 (15%)

Query: 81  VHSAKDMPTKLLKGLQISAYLPREDIRDVFISHTAQSLKDLALHSVIGTSSLRRKALLL- 139
           VH  K    +L  G +++A +  E  R +  +HTA  L   AL  V+G    +  +L+  
Sbjct: 535 VHKGKVESGELKVGDEVTAEVDEERRRRLMRNHTATHLLHAALRKVLGDHVWQAGSLVDP 594

Query: 140 -RWRSDISVIDFRG-------KIETRLNK--LNNNKAHAILLAYA-----GIKRLKKEKV 184
            + R D S   ++        +IE  +N+    N       +        G   L  EK 
Sbjct: 595 EKLRFDFS--HYKALTAEELKEIERLVNEIIRENLPVKTEEMDLDEAKAKGAMALFGEKY 652

Query: 185 IKEI--LNIEDFPPSPGQGAICIETHVNNPKAQELVKVINHE 224
             E+  + I DF        +C  THV+N     L K+I+ E
Sbjct: 653 GDEVRVVEIGDFSVE-----LCGGTHVSNTGDIGLFKIISEE 689


>gnl|CDD|31280 COG1083, NeuA, CMP-N-acetylneuraminic acid synthetase [Cell
          envelope biogenesis, outer membrane].
          Length = 228

 Score = 28.3 bits (63), Expect = 2.4
 Identities = 18/51 (35%), Positives = 22/51 (43%)

Query: 37 NIVIIPLSTKGDRITNRTLTEIGGKGLFTEEIEKKLISGEIDCAVHSAKDM 87
          NI IIP       I N+ + + GGK L    IE  L S   D  V S+   
Sbjct: 4  NIAIIPARGGSKGIKNKNIRKFGGKPLIGYTIEAALNSKLFDKVVISSDSE 54


>gnl|CDD|33975 COG4252, COG4252, Predicted transmembrane sensor domain [Signal
           transduction mechanisms].
          Length = 400

 Score = 28.0 bits (62), Expect = 3.7
 Identities = 11/33 (33%), Positives = 13/33 (39%), Gaps = 2/33 (6%)

Query: 100 YLPREDIRD--VFISHTAQSLKDLALHSVIGTS 130
            +P E IR   V I  TA SL D        + 
Sbjct: 257 KVPAELIRGRIVLIGATAPSLNDYFATPYSSSL 289


>gnl|CDD|176104 cd08412, PBP2_PAO1_like, The C-terminal substrate-binding domain of
           putative LysR-type transcriptional regulator PAO1-like,
           a member of the type 2 periplasmic binding fold protein
           superfamily.  This family includes the C-terminal
           substrate domain of a putative LysR-type transcriptional
           regulator from the plant pathogen Pseudomonas aeruginosa
           PAO1and its closely related homologs. The LysR-type
           transcriptional regulators (LTTRs) are composed of two
           functional domains joined by a linker helix involved in
           oligomerization: an N-terminal HTH (helix-turn-helix)
           domain, which is responsible for the DNA-binding
           specificity, and a C-terminal substrate-binding domain,
           which is structurally homologous to the type 2
           periplasmic binding proteins. As also observed in the
           periplasmic binding proteins, the C-terminal domain of
           the bacterial transcriptional repressor undergoes a
           conformational change upon substrate binding which in
           turn changes the DNA binding affinity of the repressor. 
           The genes controlled by the LTTRs have diverse
           functional roles including amino acid biosynthesis, CO2
           fixation, antibiotic resistance, degradation of aromatic
           compounds, nodule formation of N2 fixing bacteria, and
           synthesis of virulence factors, to a name a few. The
           structural topology of this substrate-binding domain is
           most similar to that of 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.  Besides transport proteins, the PBP2
           superfamily includes the substrate-binding domains from
           ionotropic glutamate receptors, LysR-like
           transcriptional regulators, and unorthodox sensor
           proteins involved in signal transduction.
          Length = 198

 Score = 27.5 bits (62), Expect = 4.7
 Identities = 21/66 (31%), Positives = 30/66 (45%), Gaps = 7/66 (10%)

Query: 66  EEIEKKLISGEIDCAV----HSAKDMPTKLLKGLQISAYLPREDIRDVFISHTAQSLKDL 121
           EE+E+ L SGE+D A+       +D+  + L  L    +LP  D           SL DL
Sbjct: 39  EELEEGLRSGELDLALTYDLDLPEDIAFEPLARLPPYVWLP-ADHP--LAGKDEVSLADL 95

Query: 122 ALHSVI 127
           A   +I
Sbjct: 96  AAEPLI 101


>gnl|CDD|35077 COG5518, COG5518, Bacteriophage capsid portal protein [General
           function prediction only].
          Length = 492

 Score = 26.6 bits (58), Expect = 9.0
 Identities = 21/102 (20%), Positives = 41/102 (40%), Gaps = 9/102 (8%)

Query: 23  TRSSLMDVHKIPPHNIVIIPLSTKGDRITNRTLTEIGGKGLFTEEIEKKLISGEIDCAVH 82
           +R  +    ++PP      P        T R +TE   + +F  + E+K ++ +++    
Sbjct: 349 SRDKMRSAFRLPPQYTGEAPNYNGATADTARKITE---EQVF--QPERKKLARKLNGLFL 403

Query: 83  SAKDMPTKLLKGLQISAYLPREDIRDV---FISHTAQSLKDL 121
               +  + L  L+   ++  E I      FI+  A S  DL
Sbjct: 404 EVLPIQERRLA-LKGPDWIDPEVIAFALYPFITAGAVSPNDL 444


  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
   0.321    0.137    0.401 

Gapped
Lambda     K      H
   0.267   0.0690    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 3,678,839
Number of extensions: 190647
Number of successful extensions: 452
Number of sequences better than 10.0: 1
Number of HSP's gapped: 445
Number of HSP's successfully gapped: 18
Length of query: 307
Length of database: 6,263,737
Length adjustment: 94
Effective length of query: 213
Effective length of database: 4,232,491
Effective search space: 901520583
Effective search space used: 901520583
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: 57 (25.8 bits)