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)