RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddB
21,608 sequences; 5,994,473 total letters
Searching..................................................done
Query= gi|254781165|ref|YP_003065578.1| pyridoxamine 5'-phosphate
oxidase [Candidatus Liberibacter asiaticus str. psy62]
(201 letters)
>gnl|CDD|180195 PRK05679, PRK05679, pyridoxamine 5'-phosphate oxidase; Provisional.
Length = 195
Score = 258 bits (661), Expect = 7e-70
Identities = 94/189 (49%), Positives = 124/189 (65%), Gaps = 2/189 (1%)
Query: 13 FTLLSQWMQEAQSSESHDPHAVVLATADRMGFPNARVVLIKHFDQEGFVFYTNSQSPKGK 72
L +W+ EA +E +DP+A+ LAT D G P+ R+VL+K FD+ GFVFYTN +S KG+
Sbjct: 9 LALFERWLAEAVKAELNDPNAMTLATVDEDGRPSQRIVLLKGFDERGFVFYTNYESRKGR 68
Query: 73 EILENPKASLCFHWKSLARQLRVRGLVEKYCDLASDHYYASRPRESKIGAWASKQSQKMP 132
++ NPKA+L F WKSL RQ+RV G VEK SD Y+ASRPR S+IGAWASKQS+ +
Sbjct: 69 QLAANPKAALLFPWKSLERQVRVEGRVEKVSAEESDAYFASRPRGSQIGAWASKQSRPIS 128
Query: 133 SLDDLQKSVQRYSSFYQEKEIPRPVWWHGFRICPLSIEFWSERPYRLHDRLLFSRETIAG 192
S L+ + + + E+PRP W G+R+ P SIEFW RP RLHDR+L+ R+ G
Sbjct: 129 SRAALEAKFAEVKAKFAQGEVPRPPHWGGYRVVPESIEFWQGRPSRLHDRILYRRD--DG 186
Query: 193 KWTQFLLYP 201
W L P
Sbjct: 187 GWKIERLAP 195
>gnl|CDD|129649 TIGR00558, pdxH, pyridoxamine-phosphate oxidase. This model is
similar to Pyridox_oxidase from PFAM but is designed to
find only true pyridoxamine-phosphate oxidase and to
ignore the related protein PhzG involved in phenazine
biosynthesis. This protein from E. coli was
characterized as a homodimer with two FMN per dimer.
Length = 217
Score = 195 bits (498), Expect = 6e-51
Identities = 81/176 (46%), Positives = 112/176 (63%)
Query: 13 FTLLSQWMQEAQSSESHDPHAVVLATADRMGFPNARVVLIKHFDQEGFVFYTNSQSPKGK 72
L W EA + +P+A+ L+T D G P++R+VL+K D+ GFVFYTN S KG
Sbjct: 31 IDLFEIWFNEAIEARLTEPNAMTLSTVDESGRPSSRMVLLKELDERGFVFYTNYGSRKGH 90
Query: 73 EILENPKASLCFHWKSLARQLRVRGLVEKYCDLASDHYYASRPRESKIGAWASKQSQKMP 132
+I NP A+L F W L RQ+RV G VEK SD Y+ SRPR S+IGAWAS+QS +
Sbjct: 91 QIETNPNAALVFFWPDLERQVRVEGKVEKLPREESDAYFKSRPRGSRIGAWASRQSDVIS 150
Query: 133 SLDDLQKSVQRYSSFYQEKEIPRPVWWHGFRICPLSIEFWSERPYRLHDRLLFSRE 188
+ ++L+ + + +++ EIPRP +W G+R+ P IEFW RP RLHDR ++ RE
Sbjct: 151 NREELESKALKNTEKFEDAEIPRPDYWGGYRVVPEEIEFWQGRPSRLHDRFVYRRE 206
>gnl|CDD|178609 PLN03049, PLN03049, pyridoxine (pyridoxamine) 5'-phosphate oxidase;
Provisional.
Length = 462
Score = 183 bits (466), Expect = 2e-47
Identities = 84/182 (46%), Positives = 112/182 (61%), Gaps = 1/182 (0%)
Query: 13 FTLLSQWMQEAQSSESHDPHAVVLATADRMGFPNARVVLIKHFDQEGFVFYTNSQSPKGK 72
+W +A ++ +P+A+ LATA G P+AR+VL+K D+ GFV+YTN S K
Sbjct: 271 IDQFKEWFDDAVAAGLREPNAMTLATAGEDGRPSARIVLLKGVDKRGFVWYTNYDSRKAH 330
Query: 73 EILENPKASLCFHWKSLARQLRVRGLVEKYCDLASDHYYASRPRESKIGAWASKQSQKMP 132
E+ NPKASL F+W L RQ+RV G VEK + SD Y+ SRPR S+IGA SKQS +P
Sbjct: 331 ELSANPKASLVFYWDGLHRQVRVEGSVEKVSEEESDQYFHSRPRGSQIGALVSKQSTVIP 390
Query: 133 SLDDLQKSVQRYSSFYQE-KEIPRPVWWHGFRICPLSIEFWSERPYRLHDRLLFSRETIA 191
L +S + + Y + IP+P W G+R+ P IEFW R RLHDRL ++RE I
Sbjct: 391 GRHILDQSYKELEAKYADSSAIPKPKHWGGYRLKPELIEFWQGRESRLHDRLQYTREEIN 450
Query: 192 GK 193
GK
Sbjct: 451 GK 452
>gnl|CDD|178506 PLN02918, PLN02918, pyridoxine (pyridoxamine) 5'-phosphate oxidase.
Length = 544
Score = 161 bits (409), Expect = 1e-40
Identities = 75/177 (42%), Positives = 114/177 (64%), Gaps = 1/177 (0%)
Query: 18 QWMQEAQSSESHDPHAVVLATADRMGFPNARVVLIKHFDQEGFVFYTNSQSPKGKEILEN 77
+W EA ++ +P+A+ L+TA++ G P++R+VL+K D+ GFV+YTN +S KG ++ EN
Sbjct: 358 KWFDEAVAAGLREPNAMALSTANKDGKPSSRMVLLKGVDKNGFVWYTNYESQKGSDLSEN 417
Query: 78 PKASLCFHWKSLARQLRVRGLVEKYCDLASDHYYASRPRESKIGAWASKQSQKMPSLDDL 137
P A+L F+W+ L RQ+RV G V+K + S++Y+ SRPR S+IGA SKQS +P L
Sbjct: 418 PSAALLFYWEELNRQVRVEGSVQKVPESESENYFHSRPRGSQIGAIVSKQSSVVPGRHVL 477
Query: 138 QKSVQRYSSFYQEKE-IPRPVWWHGFRICPLSIEFWSERPYRLHDRLLFSRETIAGK 193
+ + Y + IP+P W G+R+ P EFW + RLHDRL +S + + GK
Sbjct: 478 YQEYKELEKKYSDGSVIPKPKNWGGYRLKPNLFEFWQGQQSRLHDRLQYSLQEVNGK 534
>gnl|CDD|151120 pfam10590, PNPOx_C, Pyridoxine 5'-phosphate oxidase C-terminal
dimerization region. Pyridoxine 5'-phosphate oxidase
(PNPOx) catalyses the terminal step in the biosynthesis
of pyridoxal 5'-phosphate (PLP), a cofactor used by many
enzymes involved in amino acid metabolism. The enzyme
oxidizes either the 4'-hydroxyl group of pyridoxine
5'-phosphate (PNP) or the 4'-primary amine of
pyridoxamine 5'-phosphate (PMP) to an aldehyde. PNPOx is
a homodimeric enzyme with one flavin mononucleotide
(FMN) molecule non-covalently bound to each subunit.
This domain represents one of the two dimerization
regions of the protein, located at the edge of the dimer
interface, at the C-terminus, being the last three beta
strands, S6, S7, and S8 along with the last three
residues to the end. In PNPOx from Myxococcus xanthus,
S6 runs from residues 178-192, S7 from 200-206 and S8
from 211-215. the extended loop, of residues 167-177 may
well be involved in the pocket formed between the two
dimers that positions the FMN molecule.
Length = 41
Score = 63.7 bits (156), Expect = 3e-11
Identities = 22/43 (51%), Positives = 27/43 (62%), Gaps = 2/43 (4%)
Query: 159 WHGFRICPLSIEFWSERPYRLHDRLLFSRETIAGKWTQFLLYP 201
W G+R+ P SIEFW RP RLHDRL ++RE W+ L P
Sbjct: 1 WGGYRVVPESIEFWQGRPSRLHDRLRYTRE--GDGWSIERLAP 41
>gnl|CDD|132706 TIGR03667, Rv3369, PPOX class probable F420-dependent enzyme,
Rv3369 family. A Genome Properties metabolic
reconstruction for F420 biosynthesis shows that
slightly over 10 percent of all prokaryotes with fully
sequenced genomes, including about two thirds of the
Actinomycetales, make F420. A variant of the Partial
Phylogenetic Profiling algorithm, SIMBAL, shows that
this protein likely binds F420 in a cleft similar to
that in which the homologous enzyme pyridoxamine
phosphate oxidase (PPOX) binds FMN.
Length = 130
Score = 29.7 bits (67), Expect = 0.55
Identities = 16/49 (32%), Positives = 22/49 (44%), Gaps = 1/49 (2%)
Query: 36 LATADRMGFPNARVVLIKHFDQEGFVFYTNSQSPKGKEILENPKASLCF 84
L T R G P V +D F+ Y+ Q+ K + I NP+ SL
Sbjct: 19 LTTVRRSGQPQPVPVWF-LWDGTEFLIYSRPQAAKLRNIRRNPRVSLHL 66
>gnl|CDD|172669 PRK14181, PRK14181, bifunctional 5,10-methylene-tetrahydrofolate
dehydrogenase/ 5,10-methylene-tetrahydrofolate
cyclohydrolase; Provisional.
Length = 287
Score = 29.4 bits (66), Expect = 0.57
Identities = 15/48 (31%), Positives = 25/48 (52%)
Query: 29 HDPHAVVLATADRMGFPNARVVLIKHFDQEGFVFYTNSQSPKGKEILE 76
H H ++ ++ +G P A +++ KH D V +SQS EIL+
Sbjct: 152 HGRHVAIVGRSNIVGKPLAALLMQKHPDTNATVTLLHSQSENLTEILK 199
>gnl|CDD|180255 PRK05783, PRK05783, hypothetical protein; Provisional.
Length = 84
Score = 25.8 bits (57), Expect = 7.2
Identities = 8/32 (25%), Positives = 15/32 (46%)
Query: 22 EAQSSESHDPHAVVLATADRMGFPNARVVLIK 53
EA S E A+ +A R+ P ++++
Sbjct: 49 EANSPEEAKELALKIAREGRLYNPIVHKIVVR 80
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
0.321 0.134 0.428
Gapped
Lambda K H
0.267 0.0654 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 3,305,360
Number of extensions: 194458
Number of successful extensions: 350
Number of sequences better than 10.0: 1
Number of HSP's gapped: 348
Number of HSP's successfully gapped: 14
Length of query: 201
Length of database: 5,994,473
Length adjustment: 89
Effective length of query: 112
Effective length of database: 4,071,361
Effective search space: 455992432
Effective search space used: 455992432
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 (21.9 bits)
S2: 55 (25.1 bits)