RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16342
(143 letters)
>gnl|CDD|238264 cd00470, PTPS, 6-pyruvoyl tetrahydropterin synthase (PTPS). Folate
derivatives are essential cofactors in the biosynthesis
of purines, pyrimidines, and amino acids, as well as
formyl-tRNA. Mammalian cells are able to utilize
pre-formed folates after uptake by a carrier-mediated
active transport system. Most microbes and plants lack
this system and must synthesize folates de novo from
guanosine triphosphate. One enzyme from this pathway is
PTPS which catalyzes the conversion of dihydroneopterin
triphosphate to 6-pyruvoyl tetrahydropterin. The
functional enzyme is a hexamer of identical subunits.
Length = 135
Score = 196 bits (499), Expect = 6e-66
Identities = 88/136 (64%), Positives = 109/136 (80%), Gaps = 1/136 (0%)
Query: 8 IGYLTRVEKFSACHRLHSPHLTDEENKITYGKCNNFHGHGHNYTVEVTLKGPISKERGMV 67
LTR FSACHRLHSP L+DEEN +GKCNN +GHGHNY VEVT++G I GMV
Sbjct: 1 SATLTRRFSFSACHRLHSPPLSDEENLEVFGKCNNPNGHGHNYKVEVTVRGEIDPVTGMV 60
Query: 68 LNINDLKVYMVDAIMVPMDHKNLDKDVPYFADVVSTSENVAIFIWNNLKKIMKEPELLYE 127
+N+ DLK + +AIM P+DHKNLD DVPYFADVVST+EN+A++IW+NL+K++ LLYE
Sbjct: 61 MNLTDLKKAIEEAIMKPLDHKNLDDDVPYFADVVSTTENLAVYIWDNLQKVLPV-GLLYE 119
Query: 128 VKLYETDKNIVLYRGE 143
VK++ETDKNIV+YRGE
Sbjct: 120 VKVHETDKNIVVYRGE 135
>gnl|CDD|232793 TIGR00039, 6PTHBS, 6-pyruvoyl tetrahydropterin synthase/QueD family
protein. This model has been downgraded from
hypothetical_equivalog to subfamily. The animal enzymes
are known to be 6-pyruvoyl tetrahydropterin synthase.
The function of the bacterial branch of the sequence
lineage had been thought to be the same, but many are
now taken to be QueD, and enzyme of queuosine
biosynthesis. Queuosine is a hypermodified base in the
wobble position of some tRNAs in most species. A new
model is built to be the QueD equivalog model [Protein
synthesis, tRNA and rRNA base modification].
Length = 124
Score = 129 bits (325), Expect = 2e-39
Identities = 52/133 (39%), Positives = 73/133 (54%), Gaps = 14/133 (10%)
Query: 11 LTRVEKFSACHRLHSPHLTDEENKITYGKCNNFHGHGHNYTVEVTLKGPISKERGMVLNI 70
+ + FSA HRL GKC N HGH+Y V+V + G + GMV++
Sbjct: 4 IHKEFSFSAAHRLPGHE----------GKCGN--LHGHSYKVDVEVSGERDPKTGMVMDF 51
Query: 71 NDLKVYMVDAIMVPMDHKNLDKDVPYFADVVSTSENVAIFIWNNLKKIMKEPELLYEVKL 130
+DLK + + I P+DHK L+ DV Y TSENVA++I++NLK+ + E L +VK
Sbjct: 52 SDLKKIVKEVIDEPLDHKLLNDDVNY--LENPTSENVAVYIFDNLKEYLIPVENLVKVKE 109
Query: 131 YETDKNIVLYRGE 143
ET I +YRG
Sbjct: 110 EETPAEIRIYRGP 122
>gnl|CDD|216384 pfam01242, PTPS, 6-pyruvoyl tetrahydropterin synthase. 6-Pyruvoyl
tetrahydrobiopterin synthase catalyzes the conversion of
dihydroneopterin triphosphate to 6-pyruvoyl
tetrahydropterin, the second of three enzymatic steps in
the synthesis of tetrahydrobiopterin from GTP. The
functional enzyme is a hexamer of identical subunits.
Length = 121
Score = 127 bits (321), Expect = 5e-39
Identities = 52/135 (38%), Positives = 77/135 (57%), Gaps = 15/135 (11%)
Query: 10 YLTRVEKFSACHRLHSPHLTDEENKITYGKCNNFHGHGHNYTVEVTLKGPISKERGMVLN 69
+T+ F A HRL GKC+ HGH NY VEVT++G E GMV++
Sbjct: 1 TITKRFHFDAAHRLPGY----------PGKCSRLHGH--NYRVEVTVEGEELDETGMVVD 48
Query: 70 INDLKVYMVDAIMVPMDHKNLDKDVPYFADVVSTSENVAIFIWNNLKKIMKEPEL-LYEV 128
+LK + ++ +DHK L+ DVP FA V T+EN+A +IW+ LK ++ + L++V
Sbjct: 49 FGELKKIL-KEVLERLDHKLLN-DVPEFAGVNPTAENIARYIWDRLKPRLQGGGVRLHKV 106
Query: 129 KLYETDKNIVLYRGE 143
+++ET N YRGE
Sbjct: 107 RVWETPTNWAEYRGE 121
>gnl|CDD|223792 COG0720, COG0720, 6-pyruvoyl-tetrahydropterin synthase [Coenzyme
metabolism].
Length = 127
Score = 77.7 bits (192), Expect = 2e-19
Identities = 42/137 (30%), Positives = 63/137 (45%), Gaps = 18/137 (13%)
Query: 11 LTRVEKFSACHRLHSPHLTDEENKITYGKCNNFHGHGHNYTVEVTLKGPISKERGMVLNI 70
+T+ F A HRL GKC HGH Y VEV ++G E GMV++
Sbjct: 5 ITKRFSFDAAHRL----------PGHPGKCGR--LHGHTYKVEVEIEGEELDEHGMVVDF 52
Query: 71 NDLKVYMVDAIMVPMDHKNLDKDVPYFADVVSTSENVAIFIWNNLKKIMKE----PELLY 126
+LK V I+ +DHK L+ D+ F T+EN+A +I++ LK ++ +
Sbjct: 53 GELKKA-VKEILDELDHKLLN-DIEEFDKENPTAENIAKWIFDRLKVVLPDEAETSAEEL 110
Query: 127 EVKLYETDKNIVLYRGE 143
+ ET + YR
Sbjct: 111 REYVAETPTSGAEYRKR 127
>gnl|CDD|234186 TIGR03367, queuosine_QueD, queuosine biosynthesis protein QueD.
Members of this protein family, closely related to
eukaryotic 6-pyruvoyl tetrahydrobiopterin synthase
enzymes, are the QueD protein of queuosine biosynthesis.
Queuosine is a hypermodified base in the wobble position
of tRNAs for Tyr, His, Asp, and Asn in many species.
This modification, although widespread, appears not to
be important for viability. The queuosine precursor made
by this enzyme may be converted instead to archeaosine
as in some Archaea [Protein synthesis, tRNA and rRNA
base modification].
Length = 91
Score = 69.5 bits (171), Expect = 1e-16
Identities = 40/107 (37%), Positives = 58/107 (54%), Gaps = 16/107 (14%)
Query: 11 LTRVEKFSACHRLHSPHLTDEENKITYGKCNNFHGHGHNYTVEVTLKGPISKERGMVLNI 70
+T+ F A HRL P GKC N HGH Y VEVT+ G + E GMV++
Sbjct: 1 ITKEFTFDAAHRL--PGYP--------GKCANLHGH--TYKVEVTVSGEVLDEAGMVMDF 48
Query: 71 NDLKVYMVDAIMVPMDHKNLDKDVPYFADVVSTSENVAIFIWNNLKK 117
+DLK V ++ +DH L+ D+P + T+EN+A +I++ LK
Sbjct: 49 SDLKAI-VKEVVDRLDHALLN-DIPGLENP--TAENLARWIYDRLKA 91
>gnl|CDD|238351 cd00651, TFold, Tunnelling fold (T-fold). The five known T-folds
are found in five different enzymes with different
functions: dihydroneopterin-triphosphate epimerase
(DHNTPE), dihydroneopterin aldolase (DHNA) , GTP
cyclohydrolase I (GTPCH-1), 6-pyrovoyl tetrahydropterin
synthetase (PTPS), and uricase (UO,uroate/urate
oxidase). They bind to substrates belonging to the
purine or pterin families, and share a fold-related
binding site with a glutamate or glutamine residue
anchoring the substrate and a lot of conserved
interactions. They also share a similar oligomerization
mode: several T-folds join together to form a
beta(2n)alpha(n) barrel, then two barrels join together
in a head-to-head fashion to made up the native enzymes.
The functional enzyme is a tetramer for UO, a hexamer
for PTPS, an octamer for DHNA/DHNTPE and a decamer for
GTPCH-1. The substrate is located in a deep and narrow
pocket at the interface between monomers. In PTPS, the
active site is located at the interface of three
monomers, two from one trimer and one from the other
trimer. In GTPCH-1, it is also located at the interface
of three subunits, two from one pentamer and one from
the other pentamer. There are four equivalent active
sites in UO, six in PTPS, eight in DHNA/DHNTPE and ten
in GTPCH-1. Each globular multimeric enzyme encloses a
tunnel which is lined with charged residues for DHNA and
UO, and with basic residues in PTPS. The N and
C-terminal ends are located on one side of the T-fold
while the residues involved in the catalytic activity
are located at the opposite side. In PTPS, UO and
DHNA/DHNTPE, the N and C-terminal extremities of the
enzyme are located on the exterior side of the
functional multimeric enzyme. In GTPCH-1, the extra
C-terminal helix places the extremity inside the tunnel.
Length = 122
Score = 29.7 bits (67), Expect = 0.30
Identities = 16/122 (13%), Positives = 28/122 (22%), Gaps = 28/122 (22%)
Query: 13 RVEKFSACHRLHSPHLTDEENKITYGKCNNFHGHGHNYTVEVTLKGPISKERGMVLNIND 72
RV+ RL G V ++ G + V
Sbjct: 5 RVKDLLKVTRLGFV------------TLERTVGQIFEVDVTLSWDGKKAAASDDVA---- 48
Query: 73 LKVYMVDAIMVPMDHKNLDKDVPYFADVVSTSENVAIFIWNNLKKIMKEPELLYEVKLYE 132
+ + I + +E +A I + + EVK+ E
Sbjct: 49 -TDTVYNTIYRLAKEYVEGS-----QLIERLAEEIAYLIAEHFLS------SVAEVKVEE 96
Query: 133 TD 134
Sbjct: 97 KK 98
>gnl|CDD|132156 TIGR03112, 6_pyr_pter_rel, 6-pyruvoyl tetrahydropterin
synthase-related domain. Members of this family are
small proteins, or small domains of larger proteins,
that occur in certain Firmicutes in the same regions as
members of families TIGR03110 and TIGR03111. Members of
TIGR03110 resemble exosortase, a proposed protein
sorting transpeptidase (see TIGR02602). TIGR03111
represents a small clade among the group 2
glycosyltransferases. Members of the current protein
family resemble eukaryotic known and prokaryotic
predicted 6-pyruvoyl tetrahydropterin synthases.
Length = 113
Score = 28.9 bits (65), Expect = 0.53
Identities = 25/81 (30%), Positives = 45/81 (55%), Gaps = 4/81 (4%)
Query: 41 NNFHGHGHNYTVEVTLKGPISKERGMVLNINDLKVYMVDAIMVPMDHKNLDKDVPYFADV 100
N G+ H +T E+T+ I KE +L ND++ V+ + P +K L+ D+ F +
Sbjct: 16 NGVRGNKHPHTWEITIF-VIKKEDKFIL-FNDVEKK-VEKYLKPYQNKYLN-DLEPFDKI 71
Query: 101 VSTSENVAIFIWNNLKKIMKE 121
T EN+ + ++ +KK++KE
Sbjct: 72 NPTLENIGDYFFDEIKKLLKE 92
>gnl|CDD|227193 COG4856, COG4856, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 403
Score = 29.0 bits (65), Expect = 0.99
Identities = 19/74 (25%), Positives = 26/74 (35%), Gaps = 6/74 (8%)
Query: 28 LTDEENKITYGKCNNFHGHGHNYTVEVTLKGPISKERGMVLNIN-----DLKVYMVDAIM 82
LTD + Y + + G TV VTLKGP S + DL V
Sbjct: 49 LTDVPVDVLYDS-DKYFISGQPETVTVTLKGPNSIVLKSEKPEDFKVVADLTHAGVGTHE 107
Query: 83 VPMDHKNLDKDVPY 96
V + + L +
Sbjct: 108 VKLQVEGLPDGLTV 121
>gnl|CDD|227423 COG5092, NMT1, N-myristoyl transferase [Lipid metabolism].
Length = 451
Score = 28.8 bits (64), Expect = 1.1
Identities = 12/60 (20%), Positives = 19/60 (31%), Gaps = 3/60 (5%)
Query: 39 KCNNFHGHGHNYTVEVTLKGPISKERGMVLNINDLKVYMVDAIMVPMDHKNLDKDVPYFA 98
+ YT L P+S+ R +N K+YM +P K+
Sbjct: 196 VDGIWRAV---YTAGTELPSPVSQGRYYHRPLNWKKLYMCGFSGLPDGRTEKVKEARNAL 252
>gnl|CDD|173472 PTZ00192, PTZ00192, 60S ribosomal protein L13; Provisional.
Length = 218
Score = 28.4 bits (63), Expect = 1.2
Identities = 13/30 (43%), Positives = 19/30 (63%)
Query: 63 ERGMVLNINDLKVYMVDAIMVPMDHKNLDK 92
E GM +N+ LK YM ++ PM+HK + K
Sbjct: 111 EEGMNVNVQRLKTYMSKLVLFPMNHKKVQK 140
>gnl|CDD|241244 cd01208, PTB_X11, X11-like Phosphotyrosine-binding (PTB) domain.
The function of the neuronal protein X11 is unknown to
date. X11 has a PTB domain followed by two PDZ domains.
PTB domains have a common PH-like fold and are found in
various eukaryotic signaling molecules. This domain was
initially shown to binds peptides with a NPXY motif with
differing requirements for phosphorylation of the
tyrosine, although more recent studies have found that
some types of PTB domains can bind to peptides lack
tyrosine residues altogether. In contrast to SH2
domains, which recognize phosphotyrosine and adjacent
carboxy-terminal residues, PTB-domain binding
specificity is conferred by residues amino-terminal to
the phosphotyrosine. PTB domains are classified into
three groups: phosphotyrosine-dependent Shc-like,
phosphotyrosine-dependent IRS-like, and
phosphotyrosine-independent Dab-like PTB domains. This
cd is part of the Dab-like subgroup.
Length = 161
Score = 27.6 bits (62), Expect = 2.0
Identities = 19/50 (38%), Positives = 24/50 (48%), Gaps = 12/50 (24%)
Query: 51 TVEVTLKGPISKERGMVLNINDLKVYMVDAIMVPMDHKNLDKDVPYFADV 100
+ EV L IS ER VLN D + M MDH L + + Y AD+
Sbjct: 52 STEVDLF--ISTERIKVLN-ADTQETM-------MDHA-L-RTISYIADI 89
>gnl|CDD|218286 pfam04840, Vps16_C, Vps16, C-terminal region. This protein forms
part of the Class C vacuolar protein sorting (Vps)
complex. Vps16 is essential for vacuolar protein
sorting, which is essential for viability in plants, but
not yeast. The Class C Vps complex is required for
SNARE-mediated membrane fusion at the lysosome-like
yeast vacuole. It is thought to play essential roles in
membrane docking and fusion at the Golgi-to-endosome and
endosome-to-vacuole stages of transport. The role of
VPS16 in this complex is not known.
Length = 319
Score = 27.4 bits (61), Expect = 2.6
Identities = 12/46 (26%), Positives = 18/46 (39%), Gaps = 5/46 (10%)
Query: 3 SSKVPIGYLTRVEKFSACHRLHS-----PHLTDEENKITYGKCNNF 43
S K PIGY+ V + P L+ +E Y + +F
Sbjct: 233 SKKSPIGYMPFVTYCLSQGNKDEAKKYIPRLSYQEKVKAYVEVGDF 278
>gnl|CDD|224588 COG1674, FtsK, DNA segregation ATPase FtsK/SpoIIIE and related
proteins [Cell division and chromosome partitioning].
Length = 858
Score = 27.5 bits (61), Expect = 3.1
Identities = 13/57 (22%), Positives = 26/57 (45%), Gaps = 5/57 (8%)
Query: 71 NDLKVYMVDAIMVPMDHKNLDKDVPYFADVVSTSENVAIFIWNNLKKIMKEPELLYE 127
+++ Y++D M+ + D +P+ D V T E L +++ E E Y+
Sbjct: 561 EEVRFYIIDPKMLELA--AYD-GLPHLGDPVVTDE--KEKAEKALAELVAEMERRYK 612
>gnl|CDD|184712 PRK14501, PRK14501, putative bifunctional trehalose-6-phosphate
synthase/HAD hydrolase subfamily IIB; Provisional.
Length = 726
Score = 26.0 bits (58), Expect = 8.0
Identities = 12/39 (30%), Positives = 15/39 (38%), Gaps = 6/39 (15%)
Query: 13 RVEKFSACHRLHSPHLTDEENKITY-GKCNN-----FHG 45
R+E L L+ EE Y G CN+ FH
Sbjct: 63 RIEPRLEELGLVPVFLSAEEVDRYYEGFCNSTLWPLFHY 101
>gnl|CDD|193564 cd08017, M20_IAA_Hyd, M20 Peptidase Indole-3-acetic acid amino acid
hydrolase. Peptidase M20 family, Plant Aminoacyclase-1
indole-3-acetic-L-aspartic acid hydrolase (IAA-Asp
hydrolase; IAAspH; IAAH; IAA amidohydrolase; EC 3.5.1.-)
subfamily. IAAspH hydrolyzes indole-3-acetyl-N-aspartic
acid (IAA or auxin) to indole-3-acetic acid. Genes
encoding IAA-amidohydrolases were first cloned from
Arabidopsis; ILR1, IAR3, ILL1 and ILL2 encode active
IAA- amino acid hydrolases, and three additional
amidohydrolase-like genes (ILL3, ILL5, ILL6) have been
isolated. In higher plants, the growth regulator
indole-3-acetic acid (IAA or auxin) is found both free
and conjugated via amide bonding to a variety of amino
acids and peptides, and via an ester linkage to
carbohydrates. IAA-Asp conjugates are involved in
homeostatic control, protection, storing and subsequent
use of free IAA. IAA-Asp is also found in some plants as
a unique intermediate for entering into IAA
non-decarboxylative oxidative pathway. IAA
amidohydrolase cleaves the amide bond between the auxin
and the conjugated amino acid. Enterobacter agglomerans
IAAspH has very strong enzyme activity and substrate
specificity towards IAA-Asp, although its substrate
affinity is weaker compared to Arabidopsis enzymes of
the ILR1 gene family. Enhanced IAA-hydrolase activity
has been observed during clubroot disease in Chinese
cabbage.
Length = 377
Score = 26.1 bits (58), Expect = 8.5
Identities = 9/27 (33%), Positives = 13/27 (48%)
Query: 12 TRVEKFSACHRLHSPHLTDEENKITYG 38
R E + H LHSP+ +E + G
Sbjct: 338 IRNETAGSVHSLHSPYFFLDEEVLPVG 364
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
0.318 0.136 0.403
Gapped
Lambda K H
0.267 0.0762 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,139,791
Number of extensions: 622428
Number of successful extensions: 500
Number of sequences better than 10.0: 1
Number of HSP's gapped: 486
Number of HSP's successfully gapped: 24
Length of query: 143
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 56
Effective length of database: 7,078,804
Effective search space: 396413024
Effective search space used: 396413024
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 54 (24.5 bits)