RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14695
(241 letters)
>gnl|CDD|211586 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
[Biosynthesis of cofactors, prosthetic groups, and
carriers, Pyridoxine].
Length = 190
Score = 114 bits (288), Expect = 1e-31
Identities = 60/213 (28%), Positives = 103/213 (48%), Gaps = 36/213 (16%)
Query: 40 DPMQLFKSWFTHHSELHSDSNLV-ANVMNVSTASKDGRVNSRSLILRRLDEDGFVIMTDG 98
DP++ F+ WF E + L N M ++T DGR ++R ++L+ DE GFV T+
Sbjct: 1 DPIEQFERWFEEAIE----AELPEPNAMTLATVDADGRPSARIVLLKGFDERGFVFYTNY 56
Query: 99 RSSKSKDLKENPNAAFTFLWINNVDGLYLARQIRIAGKVVQLETSNWIDIYEAE------ 152
S K ++L NP AA F W + L RQ+RI G+V ++ E++
Sbjct: 57 ESRKGQELAANPKAALLFPWHS------LERQVRIEGRVEKVSRE------ESDAYFASR 104
Query: 153 PLFCKIRAYVCHQGQPVDWDTHKKNHDELLSKFEK-----GQHDLARPDHVIAYKLFPTF 207
P +I A+ Q +P+ + +EL +F + ++ RP+H Y++ P
Sbjct: 105 PRGSQIGAWASQQSRPIA------SREELEERFAELKARFPDGEVPRPEHWGGYRVVPDE 158
Query: 208 MDFYESHGLKIADRLKYVRDNENAKDWECTRIA 240
++F++ ++ DR +Y RD + W R+A
Sbjct: 159 IEFWQGRPSRLHDRFRYRRDGDG--SWRIERLA 189
>gnl|CDD|215550 PLN03049, PLN03049, pyridoxine (pyridoxamine) 5'-phosphate oxidase;
Provisional.
Length = 462
Score = 117 bits (294), Expect = 2e-30
Identities = 61/209 (29%), Positives = 104/209 (49%), Gaps = 22/209 (10%)
Query: 39 ADPMQLFKSWFTHHSELHSDSNLVA-----NVMNVSTASKDGRVNSRSLILRRLDEDGFV 93
ADP+ FK WF D + A N M ++TA +DGR ++R ++L+ +D+ GFV
Sbjct: 268 ADPIDQFKEWF--------DDAVAAGLREPNAMTLATAGEDGRPSARIVLLKGVDKRGFV 319
Query: 94 IMTDGRSSKSKDLKENPNAAFTFLWINNVDGLYLARQIRIAGKVVQLETSNWIDIYEAEP 153
T+ S K+ +L NP A+ F W DGL+ RQ+R+ G V ++ + + P
Sbjct: 320 WYTNYDSRKAHELSANPKASLVFYW----DGLH--RQVRVEGSVEKVSEEESDQYFHSRP 373
Query: 154 LFCKIRAYVCHQGQPV-DWDTHKKNHDELLSKFEKGQHDLARPDHVIAYKLFPTFMDFYE 212
+I A V Q + +++ EL +K+ + +P H Y+L P ++F++
Sbjct: 374 RGSQIGALVSKQSTVIPGRHILDQSYKELEAKYADSSA-IPKPKHWGGYRLKPELIEFWQ 432
Query: 213 SHGLKIADRLKYVR-DNENAKDWECTRIA 240
++ DRL+Y R + W+ R+A
Sbjct: 433 GRESRLHDRLQYTREEINGKSVWKIDRLA 461
>gnl|CDD|223337 COG0259, PdxH, Pyridoxamine-phosphate oxidase [Coenzyme
metabolism].
Length = 214
Score = 107 bits (270), Expect = 7e-29
Identities = 63/231 (27%), Positives = 110/231 (47%), Gaps = 26/231 (11%)
Query: 18 QANPLTNLA-EMT--GIQKIDPIPADPMQLFKSWFTHHSELHSDSNLVANVMNVSTASKD 74
+ L N+ E T G+++ D A+P+ LF+ W E N M ++T +
Sbjct: 1 MMDVLANIRREYTKAGLREADLPTANPLTLFRRWL---EEAIRAEVNEPNAMTLATVDEQ 57
Query: 75 GRVNSRSLILRRLDEDGFVIMTDGRSSKSKDLKENPNAAFTFLWINNVDGLYLARQIRIA 134
GR +SR ++L+ LDE GFV T+ S K ++L NP AA F W L RQ+R+
Sbjct: 58 GRPSSRIVLLKELDERGFVFYTNYGSRKGRELAANPYAALLFPWKE------LERQVRVE 111
Query: 135 GKVVQLETSNWIDIYEAEPLFCKIRAYVCHQGQPVDWDTHKKNHDELLSKFEK-----GQ 189
G+V ++ + + P +I A+ Q +P+ + L +K +
Sbjct: 112 GRVERVSDEESDAYFASRPRGSQIGAWASKQSRPI------ASRAALEAKVAELTAKFAD 165
Query: 190 HDLARPDHVIAYKLFPTFMDFYESHGLKIADRLKYVRDNENAKDWECTRIA 240
++ RP H +++ P ++F++ ++ DRL+Y RD+ W+ R+A
Sbjct: 166 GEIPRPPHWGGFRIVPESIEFWQGRPSRLHDRLRYRRDDG---GWKIERLA 213
>gnl|CDD|215496 PLN02918, PLN02918, pyridoxine (pyridoxamine) 5'-phosphate oxidase.
Length = 544
Score = 103 bits (258), Expect = 2e-25
Identities = 67/215 (31%), Positives = 107/215 (49%), Gaps = 30/215 (13%)
Query: 37 IPADPMQLFKSWFTHHSELHSDSNLVA-----NVMNVSTASKDGRVNSRSLILRRLDEDG 91
+ DP F+ WF D + A N M +STA+KDG+ +SR ++L+ +D++G
Sbjct: 348 VETDPTDQFRKWF--------DEAVAAGLREPNAMALSTANKDGKPSSRMVLLKGVDKNG 399
Query: 92 FVIMTDGRSSKSKDLKENPNAAFTFLWINNVDGLYLARQIRIAGKVVQLETSNWIDIYEA 151
FV T+ S K DL ENP+AA F W + L RQ+R+ G V ++ S + + +
Sbjct: 400 FVWYTNYESQKGSDLSENPSAALLFYW----EE--LNRQVRVEGSVQKVPESESENYFHS 453
Query: 152 EPLFCKIRAYVCHQ-----GQPVDWDTHKKNHDELLSKFEKGQHDLARPDHVIAYKLFPT 206
P +I A V Q G+ V + +K EL K+ G + +P + Y+L P
Sbjct: 454 RPRGSQIGAIVSKQSSVVPGRHVLYQEYK----ELEKKYSDGSV-IPKPKNWGGYRLKPN 508
Query: 207 FMDFYESHGLKIADRLKYVRDNENAKD-WECTRIA 240
+F++ ++ DRL+Y N K W+ R+A
Sbjct: 509 LFEFWQGQQSRLHDRLQYSLQEVNGKPVWKIHRLA 543
>gnl|CDD|235555 PRK05679, PRK05679, pyridoxamine 5'-phosphate oxidase; Provisional.
Length = 195
Score = 96.1 bits (240), Expect = 1e-24
Identities = 61/210 (29%), Positives = 104/210 (49%), Gaps = 27/210 (12%)
Query: 38 PADPMQLFKSWFT--HHSELHSDSNLVANVMNVSTASKDGRVNSRSLILRRLDEDGFVIM 95
PA+P+ LF+ W +EL +D N M ++T +DGR + R ++L+ DE GFV
Sbjct: 5 PAEPLALFERWLAEAVKAEL-ND----PNAMTLATVDEDGRPSQRIVLLKGFDERGFVFY 59
Query: 96 TDGRSSKSKDLKENPNAAFTFLWINNVDGLYLARQIRIAGKVVQLETSNWIDIYEAEPLF 155
T+ S K + L NP AA F W + L RQ+R+ G+V ++ + + P
Sbjct: 60 TNYESRKGRQLAANPKAALLFPWKS------LERQVRVEGRVEKVSAEESDAYFASRPRG 113
Query: 156 CKIRAYVCHQGQPVDWDTHKKNHDELLSKFEK-----GQHDLARPDHVIAYKLFPTFMDF 210
+I A+ Q +P+ + L +KF + Q ++ RP H Y++ P ++F
Sbjct: 114 SQIGAWASKQSRPIS------SRAALEAKFAEVKAKFAQGEVPRPPHWGGYRVVPESIEF 167
Query: 211 YESHGLKIADRLKYVRDNENAKDWECTRIA 240
++ ++ DR+ Y RD+ W+ R+A
Sbjct: 168 WQGRPSRLHDRILYRRDDG---GWKIERLA 194
>gnl|CDD|216385 pfam01243, Pyridox_oxidase, Pyridoxamine 5'-phosphate oxidase.
Length = 88
Score = 55.3 bits (134), Expect = 2e-10
Identities = 22/80 (27%), Positives = 34/80 (42%), Gaps = 7/80 (8%)
Query: 63 ANVMNVSTASKDGRVNSRSLILRRLDEDG-FVIMTDGRSSKSKDLKENPNAAFTFLWINN 121
N ++T DGR N + + D+ G T+ S K+++L+ENP A F
Sbjct: 12 PNAGVLATVDADGRPNVSPVGFKYGDDRGTIYFATNYDSRKARNLRENPRVALLFGD--- 68
Query: 122 VDGLYLARQIRIAGKVVQLE 141
L R +RI G +
Sbjct: 69 ---PELRRGVRIEGTAEIVT 85
>gnl|CDD|226105 COG3576, COG3576, Predicted flavin-nucleotide-binding protein
structurally related to pyridoxine 5'-phosphate oxidase
[General function prediction only].
Length = 173
Score = 35.9 bits (83), Expect = 0.008
Identities = 23/80 (28%), Positives = 32/80 (40%), Gaps = 7/80 (8%)
Query: 51 HHSELHSDSNLVANVMNVSTASKDGRVN-SRSLILRRLDEDGFVIMTDGRSSKSKD--LK 107
H+ E S L A ++T KDG N +R D GF I+ D ++ D L
Sbjct: 33 HYREFIQTSQLAA----LATVDKDGPPNVDPIPFAQRGDPAGFTIVIDDNTAGKTDRNLG 88
Query: 108 ENPNAAFTFLWINNVDGLYL 127
NP + N L+L
Sbjct: 89 NNPKITLRNILRNRRALLFL 108
>gnl|CDD|221760 pfam12766, Pyridox_oxase_2, Pyridoxamine 5'-phosphate oxidase.
Pyridoxamine 5'-phosphate oxidase catalyzes the
oxidation of pyridoxamine-5-P (PMP) and pyridoxine-5-P
(PNP) to pyridoxal-5-P (PLP), the terminal step in the
de novo biosynthesis of PLP in Escherichia coli and part
of the salvage pathway of this coenzyme in both E. coli
and mammalian cells. This region is the flavoprotein
FMN-binding domain.
Length = 98
Score = 32.9 bits (76), Expect = 0.027
Identities = 21/74 (28%), Positives = 26/74 (35%), Gaps = 16/74 (21%)
Query: 71 ASKDGRVNSRSLILR-RLDEDG---FVIMTDGRSSKSKDLKENPNAAFTFLWINNVDGLY 126
DGR R+++ R L ED TD RS K L+ NP + Y
Sbjct: 30 DPSDGRPRVRTVVFRGFLFEDESDVLTFTTDARSEKVAQLESNPAVEACW---------Y 80
Query: 127 LAR---QIRIAGKV 137
Q RI G
Sbjct: 81 FPDTREQFRIRGTA 94
>gnl|CDD|188541 TIGR04026, PPOX_FMN_cyano, PPOX class probable FMN-dependent
enzyme, alr4036 family. Members of the PPOX family (see
pfam01243) may contain either FMN or F420 as cofactor.
This subfamily described here is widespread in
Cyanobacteria and plants, and is named for alr4036 from
Nostoc sp. PCC 7120. The family consists mostly of
proteins from species that lack the capability to
synthesize F420, so it is probable that all members bind
FMN rather than F420 [Unknown function, Enzymes of
unknown specificity].
Length = 185
Score = 33.0 bits (76), Expect = 0.068
Identities = 24/79 (30%), Positives = 38/79 (48%), Gaps = 14/79 (17%)
Query: 70 TASKDGRVNSRSLILRR-LDEDGFVIMTDGRSSKSKDLKENPNAAFTFLWINNVDGLYLA 128
T + DG +R+++ R D + + TD RS K + L +NPNA W Y
Sbjct: 28 TVTSDGTPRNRTVVFRGWGDSNQLELFTDARSEKIEQLAQNPNAE--ICW-------YFP 78
Query: 129 R---QIRIAGKVVQLETSN 144
+ Q R+ GK + L T++
Sbjct: 79 KTREQFRLRGK-LTLVTAD 96
>gnl|CDD|233818 TIGR02306, RNA_lig_DRB0094, RNA ligase, DRB0094 family. The member
of this family from Deinococcus radiodurans, a species
that withstands and recovers from extensive radiation or
dessication damage, is an apparent RNA ligase. It
repairs RNA stand breaks in nicked DNA:RNA and RNA:RNA
but not DNA:DNA duplexes. It has adenylyltransferase
activity associated with the C-terminal domain. Related
proteins also in this family are found in Streptomyces
avermitilis MA-4680 and in bacteriophage 44RR2.8t. The
phage example is unsurprising since one mechanism of
host cell defense against phage is cleavage and
inactivation of certain tRNA molecules. A fungal
sequence from Neurospora crassa scores between trusted
and noise cutofffs and may be similar in function.
Length = 341
Score = 31.0 bits (70), Expect = 0.45
Identities = 23/128 (17%), Positives = 46/128 (35%), Gaps = 15/128 (11%)
Query: 23 TNLAEMTGIQK----IDPIPADPMQLFKSWFTHHSELHSD---SNLVANVMNVSTASKDG 75
++AEM GI K + F + E + T G
Sbjct: 110 KDIAEMLGITKWEPPQPGTMCGEGETFPIFIPKTDEERCQNYFNRFKEGEKVAKTEKLHG 169
Query: 76 RVNSRSLILRRLDEDGFVIMTDGRSSKSKDLKENPN-----AAFTFLWINNVDGLYLARQ 130
+ + DE+ F++++ G +S++ L+EN + A + ++ L
Sbjct: 170 ---TSITVAWVTDEERFLVLSKGVASRNLVLRENADNKYWKAVENYQIVDRAKAAELRMS 226
Query: 131 IRIAGKVV 138
+ I G+V+
Sbjct: 227 VAIFGEVM 234
>gnl|CDD|233114 TIGR00752, slp, outer membrane lipoprotein, Slp family. Slp
superfamily members are present in the Gram-negative
gamma proteobacteria Escherichia coli, which also
contains a close paralog, Haemophilus influenzae and
Pasteurella multocida and Vibrio cholera. The known
members of the family to date share a motif LX[GA]C near
the N-terminus, which is compatible with the possibility
that the protein is modified into a lipoprotein with Cys
as the new N-terminus. Slp from Escherichia coli is
known to be a lipoprotein of the outer membrane and to
be expressed in response to carbon starvation [Cell
envelope, Other].
Length = 182
Score = 30.6 bits (69), Expect = 0.52
Identities = 12/48 (25%), Positives = 22/48 (45%), Gaps = 1/48 (2%)
Query: 92 FVIMTDGRSSKSKDLK-ENPNAAFTFLWINNVDGLYLARQIRIAGKVV 138
G + K +K E P + +++ ++ LY+ + R GKVV
Sbjct: 11 LCFGLTGCIAPPKGIKGERPFSQNSYVEVSPQPLLYVGQTARFGGKVV 58
>gnl|CDD|238872 cd01834, SGNH_hydrolase_like_2, SGNH_hydrolase subfamily. SGNH
hydrolases are a diverse family of lipases and
esterases. The tertiary fold of the enzyme is
substantially different from that of the alpha/beta
hydrolase family and unique among all known hydrolases;
its active site closely resembles the Ser-His-Asp(Glu)
triad found in other serine hydrolases.
Length = 191
Score = 28.8 bits (65), Expect = 1.9
Identities = 8/49 (16%), Positives = 17/49 (34%)
Query: 167 QPVDWDTHKKNHDELLSKFEKGQHDLARPDHVIAYKLFPTFMDFYESHG 215
D ++ L+ + +LA + V LF + ++ G
Sbjct: 117 ANEDPLPDGAEYNANLAAYADAVRELAAENGVAFVDLFTPMKEAFQKAG 165
>gnl|CDD|107363 cd06368, PBP1_iGluR_non_NMDA_like, N-terminal
leucine/isoleucine/valine-binding protein (LIVBP)-like
domain of the non-NMDA (N-methyl-d-asparate) subtypes of
ionotropic glutamate receptors. N-terminal
leucine/isoleucine/valine-binding protein (LIVBP)-like
domain of the non-NMDA (N-methyl-d-asparate) subtypes of
ionotropic glutamate receptors. While this N-terminal
domain belongs to the periplasmic-binding fold type I
superfamily, the glutamate-binding domain of the iGluR
is structurally homologous to the periplasmic-binding
fold type II. The LIVBP-like domain of iGluRs is thought
to play a role in the initial assembly of iGluR
subunits, but it is not well understood how this domain
is arranged and functions in intact iGluR. Glutamate
mediates the majority of excitatory synaptic
transmission in the central nervous system via two broad
classes of ionotropic receptors, characterized by their
response to glutamate agonists: N-methyl-d -aspartate
(NMDA) and non-NMDA receptors. NMDA receptors have
intrinsically slow kinetics, are highly permeable to
Ca2+, and are blocked by extracellular Mg2+ in a
voltage-dependent manner. Non-NMDA receptors have faster
kinetics, are most often only weakly permeable to Ca2+,
and are not blocked by extracellular Mg2+. While
non-NMDA receptors typically mediate excitatory synaptic
responses at resting membrane potentials, NMDA receptors
contribute several forms of synaptic plasticity and are
thought to play an important role in the development of
synaptic pathways. Non-NMDA receptors include
alpha-amino-3-hydroxy-5-methyl-4-isoxazole proprionate
(AMPA) and kainate receptors.
Length = 324
Score = 28.0 bits (63), Expect = 4.6
Identities = 8/48 (16%), Positives = 17/48 (35%), Gaps = 2/48 (4%)
Query: 24 NLAEMTGIQKIDPIPADPMQLFKSWFTHHSELHSDSNLVANVMNVSTA 71
+TG + +DP + + + W + S L + +A
Sbjct: 230 GGVNITGFRLVDPDNPEVQKFIQRWERSDHRICPGSGL--KPIKTESA 275
>gnl|CDD|237457 PRK13647, cbiO, cobalt transporter ATP-binding subunit;
Provisional.
Length = 274
Score = 27.4 bits (61), Expect = 6.3
Identities = 10/39 (25%), Positives = 22/39 (56%), Gaps = 2/39 (5%)
Query: 110 PNAAFTFLWINNVDGLYLARQ--IRIAGKVVQLETSNWI 146
PN A + +++G+YL ++ +++ G+ V E W+
Sbjct: 39 PNGAGKSTLLLHLNGIYLPQRGRVKVMGREVNAENEKWV 77
>gnl|CDD|240076 cd04725, OMP_decarboxylase_like, Orotidine 5'-phosphate
decarboxylase (ODCase) is a dimeric enzyme that
decarboxylates orotidine 5'-monophosphate (OMP) to form
uridine 5'-phosphate (UMP), an essential step in the
pyrimidine biosynthetic pathway. In mammals, UMP
synthase contains two domains: the orotate
phosphoribosyltransferase (OPRTase) domain that
catalyzes the transfer of phosphoribosyl
5'-pyrophosphate (PRPP) to orotate to form OMP, and the
orotidine-5'-phosphate decarboxylase (ODCase) domain
that decarboxylates OMP to form UMP.
Length = 216
Score = 27.1 bits (61), Expect = 6.9
Identities = 7/28 (25%), Positives = 14/28 (50%), Gaps = 3/28 (10%)
Query: 196 DHVIAYKLFPTFMDFYESHGLKIADRLK 223
+V A K ++ +E+ G +I L+
Sbjct: 22 PYVCAVK---VGLELFEAAGPEIVKELR 46
>gnl|CDD|211905 TIGR04170, RNR_1b_NrdE, ribonucleoside-diphosphate reductase, class
1b, alpha subunit. Members of this family are NrdE, the
alpha subunit of class 1b ribonucleotide reductase. This
form uses a dimanganese moiety associated with a
tyrosine radical to reduce the cellular requirement for
iron.
Length = 698
Score = 27.0 bits (60), Expect = 9.5
Identities = 15/39 (38%), Positives = 21/39 (53%), Gaps = 4/39 (10%)
Query: 196 DHVIAYKL-FPTFM---DFYESHGLKIADRLKYVRDNEN 230
+H A K FP+FM FY S+ LK D +Y+ E+
Sbjct: 76 EHAYASKFRFPSFMGAFKFYTSYALKTNDGKRYLERYED 114
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.319 0.134 0.409
Gapped
Lambda K H
0.267 0.0783 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 12,323,113
Number of extensions: 1137838
Number of successful extensions: 1006
Number of sequences better than 10.0: 1
Number of HSP's gapped: 994
Number of HSP's successfully gapped: 21
Length of query: 241
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 147
Effective length of database: 6,768,326
Effective search space: 994943922
Effective search space used: 994943922
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: 58 (26.0 bits)