RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254781032|ref|YP_003065445.1| hypothetical protein
CLIBASIA_04670 [Candidatus Liberibacter asiaticus str. psy62]
(118 letters)
>gnl|CDD|144727 pfam01242, PTPS, 6-pyruvoyl tetrahydropterin synthase. 6-Pyruvoyl
tetrahydrobiopterin synthase catalyses 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 = 120
Score = 143 bits (363), Expect = 9e-36
Identities = 60/122 (49%), Positives = 81/122 (66%), Gaps = 8/122 (6%)
Query: 2 KITQAFTFEAAHRLPRVPKTHKCHRMHGHSYRVELVMEGDVDPKTGFVDDFFNIEQYFSP 61
IT+ F F+AAHRLP P KC R+HGH+YRVE+ +EG+ +TG V DF +++
Sbjct: 1 TITKRFRFDAAHRLPGYP--GKCSRLHGHNYRVEVTVEGEELDETGMVVDFGELKKILKE 58
Query: 62 LLEKLDHHCLNEIEELE--NPTAENIAIWIWKRLSTSLS----ILSSVRVYETPMSWVEY 115
+LE+LDH LN++ E NPTAENIA +IW RL L+ LS VR++ETP +W EY
Sbjct: 59 VLERLDHKLLNDVPEFAGLNPTAENIARYIWDRLKPRLNGGGVRLSKVRLWETPTNWAEY 118
Query: 116 QG 117
+G
Sbjct: 119 RG 120
>gnl|CDD|31064 COG0720, COG0720, 6-pyruvoyl-tetrahydropterin synthase [Coenzyme
metabolism].
Length = 127
Score = 106 bits (265), Expect = 2e-24
Identities = 56/126 (44%), Positives = 76/126 (60%), Gaps = 11/126 (8%)
Query: 1 MKITQAFTFEAAHRLPRVPKTHKCHRMHGHSYRVELVMEGDVDPKTGFVDDFFNIEQYFS 60
IT+ F+F+AAHRLP P KC R+HGH+Y+VE+ +EG+ + G V DF +++
Sbjct: 3 RGITKRFSFDAAHRLPGHPG--KCGRLHGHTYKVEVEIEGEELDEHGMVVDFGELKKAVK 60
Query: 61 PLLEKLDHHCLNEIEEL--ENPTAENIAIWIWKRLSTSLSILSSVR-------VYETPMS 111
+L++LDH LN+IEE ENPTAENIA WI+ RL L + V ETP S
Sbjct: 61 EILDELDHKLLNDIEEFDKENPTAENIAKWIFDRLKVVLPDEAETSAEELREYVAETPTS 120
Query: 112 WVEYQG 117
EY+
Sbjct: 121 GAEYRK 126
>gnl|CDD|29761 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 = 100 bits (250), Expect = 9e-23
Identities = 42/131 (32%), Positives = 71/131 (54%), Gaps = 16/131 (12%)
Query: 3 ITQAFTFEAAHRLPRVPKT--------HKCH--RMHGHSYRVELVMEGDVDPKTGFVDDF 52
+T+ F+F A HRL P + KC+ HGH+Y+VE+ + G++DP TG V +
Sbjct: 4 LTRRFSFSACHRLHSPPLSDEENLEVFGKCNNPNGHGHNYKVEVTVRGEIDPVTGMVMNL 63
Query: 53 FNIEQY-FSPLLEKLDHHCLNEIEE---LENPTAENIAIWIWKRLSTSL--SILSSVRVY 106
++++ +++ LDH L++ T EN+A++IW L L +L V+V+
Sbjct: 64 TDLKKAIEEAIMKPLDHKNLDDDVPYFADVVSTTENLAVYIWDNLQKVLPVGLLYEVKVH 123
Query: 107 ETPMSWVEYQG 117
ET + V Y+G
Sbjct: 124 ETDKNIVVYRG 134
>gnl|CDD|39308 KOG4105, KOG4105, KOG4105, 6-pyruvoyl tetrahydrobiopterin synthase
[Coenzyme transport and metabolism].
Length = 141
Score = 68.2 bits (166), Expect = 5e-13
Identities = 40/132 (30%), Positives = 70/132 (53%), Gaps = 17/132 (12%)
Query: 3 ITQAFTFEAAHRL--PRVPKTH------KCHRM--HGHSYRVELVMEGDVDPKTGFVDDF 52
+ + +F AAHRL ++ KC+ HGH+Y V++ + G++DP TG V +
Sbjct: 9 MERRDSFSAAHRLHSEKLSDAENLETFGKCNNSNGHGHNYVVKVTVRGEIDPTTGMVYNL 68
Query: 53 FNIEQYFSPLLEK-LDHHCLN-EIEELEN--PTAENIAIWIWKRLSTSL---SILSSVRV 105
+++ ++ LDH L+ ++E T EN+A++IW L + L S+L V++
Sbjct: 69 AKLKKEMELVIMTRLDHKNLDKDVEYFATTVSTTENVAVYIWDNLKSVLSNPSVLYKVKI 128
Query: 106 YETPMSWVEYQG 117
ETP + Y+G
Sbjct: 129 EETPKNIFTYKG 140
>gnl|CDD|29764 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 = 30.8 bits (69), Expect = 0.089
Identities = 19/101 (18%), Positives = 33/101 (32%), Gaps = 11/101 (10%)
Query: 9 FEAAHRLPRVPKTHKCHRMHGHSYRVELVMEGDVDPKTGFVDDFFNIEQYFSPLLEKLDH 68
RL V ++ V L +G + V + ++ +
Sbjct: 9 LLKVTRLGFVTLERTVGQIF--EVDVTLSWDGKKAAASDDVAT----DTVYNTIYRLAKE 62
Query: 69 HCLNEIEELENPTAENIAIWIWKRLSTSLSILSSVRVYETP 109
+ E +L AE IA I + LS ++ V+V E
Sbjct: 63 Y--VEGSQLIERLAEEIAYLIAEHF---LSSVAEVKVEEKK 98
>gnl|CDD|36662 KOG1449, KOG1449, KOG1449, Predicted Rho GTPase-activating protein
CdGAPr [Signal transduction mechanisms].
Length = 670
Score = 26.3 bits (57), Expect = 2.2
Identities = 17/78 (21%), Positives = 28/78 (35%), Gaps = 2/78 (2%)
Query: 30 HSYRVELVMEGDVDPKTGFVDDFFNIEQYFSPLLEKLDHHCLNEIEELENPTAENIAIWI 89
+ V+ +G P FFN+ S + K L E+ P + A +
Sbjct: 132 LVFGVQPTNQGKSSPVLRSWRSFFNLGASLSDCIFKRRFSRLPELP--PPPQGASAAQML 189
Query: 90 WKRLSTSLSILSSVRVYE 107
RL+ + LSS+
Sbjct: 190 TPRLAKYMETLSSLVDSN 207
>gnl|CDD|35161 COG5602, SIN3, Histone deacetylase complex, SIN3 component [Chromatin
structure and dynamics].
Length = 1163
Score = 25.8 bits (56), Expect = 2.9
Identities = 13/63 (20%), Positives = 21/63 (33%), Gaps = 1/63 (1%)
Query: 37 VMEGDVDPKTGFVDDFFNIEQYFSPLLEKLDHHCLNEIEELENPTAENIAIWIWKRLSTS 96
+ D K + F + S ++ E+E L NP E + + W S
Sbjct: 949 LHPITYDIKYIAKSELFEMNSAASSKRKQDQTKYRLEVESLLNPD-EILFRFCWINKFKS 1007
Query: 97 LSI 99
I
Sbjct: 1008 FGI 1010
>gnl|CDD|48605 cd03056, GST_N_4, GST_N family, unknown subfamily 4; composed of
uncharacterized bacterial proteins with similarity to
GSTs. GSTs are cytosolic dimeric proteins involved in
cellular detoxification by catalyzing the conjugation
of glutathione (GSH) with a wide range of endogenous
and xenobiotic alkylating agents, including
carcinogens, therapeutic drugs, environmental toxins
and products of oxidative stress. GSTs also show GSH
peroxidase activity and are involved in the synthesis
of prostaglandins and leukotrienes. The GST fold
contains an N-terminal TRX-fold domain and a C-terminal
alpha helical domain, with an active site located in a
cleft between the two domains..
Length = 73
Score = 25.1 bits (55), Expect = 4.3
Identities = 7/34 (20%), Positives = 14/34 (41%), Gaps = 2/34 (5%)
Query: 24 CHRMHGHSYRVELVME-GDVDPKTGFVDDFFNIE 56
+ G+ Y+V L++ + + V D E
Sbjct: 5 GFPLSGNCYKVRLLLALLGIPYEWVEV-DILKGE 37
>gnl|CDD|30565 COG0216, PrfA, Protein chain release factor A [Translation,
ribosomal structure and biogenesis].
Length = 363
Score = 25.1 bits (55), Expect = 4.6
Identities = 18/51 (35%), Positives = 26/51 (50%), Gaps = 7/51 (13%)
Query: 9 FEA-AHRLPRVPKTHKCHRMHGHSYRV------ELVMEGDVDPKTGFVDDF 52
FE+ HR+ RVP T R+H + V E V E +++PK +D F
Sbjct: 180 FESGVHRVQRVPATESQGRIHTSAATVAVLPEVEEVEEIEINPKDLRIDTF 230
>gnl|CDD|146335 pfam03641, Lysine_decarbox, Possible lysine decarboxylase. The
members of this family share a highly conserved motif
PGGXGTXXE that is probably functionally important. This
family includes proteins annotated as lysine
decarboxylases, although the evidence for this is not
clear.
Length = 130
Score = 24.9 bits (55), Expect = 5.9
Identities = 8/17 (47%), Positives = 10/17 (58%)
Query: 52 FFNIEQYFSPLLEKLDH 68
N Y+ PLLE +DH
Sbjct: 87 LLNPNGYYDPLLEFIDH 103
>gnl|CDD|133466 cd06856, GT_GPT_archaea, UDP-GlcNAc:dolichol-P GlcNAc-1-P
transferase (GPT)-like proteins in archaea. Eukaryotic
GPT catalyzes the transfer of GlcNAc-1-P from
UDP-GlcNAc to dolichol-P to form GlcNAc-P-P-dolichol.
The reaction is the first step in the assembly of
dolichol-linked oligosaccharide intermediates and is
essential for eukaryotic N-linked glycosylation.
Evidence for the existence of the N-glycosylation
pathway in archaea has emerged and genes responsible
for the pathway have been identified. A glycosyl
transferase gene Mv1751 in M. voltae encodes for the
enzyme that carries out the first step in the pathway,
the attachment of GlcNAc to a dolichol lipid carrier in
the membrane. A lethal mutation in the alg7 (GPT) gene
in Saccharomyces cerevisiae was successfully
complemented with Mv1751, the archaea gene, indicating
that eukaryotic and archaeal enzymes may use the same
substrates and are evolutionarily closer than the
bacterial enzyme, which uses a different substrate.
Length = 280
Score = 24.5 bits (54), Expect = 6.6
Identities = 6/17 (35%), Positives = 8/17 (47%)
Query: 47 GFVDDFFNIEQYFSPLL 63
G +DD + Q LL
Sbjct: 55 GLLDDILGLSQSEKVLL 71
>gnl|CDD|110523 pfam01526, Transposase_7, Transposase. This family includes
transposases of Tn3, Tn21, Tn1721, Tn2501, Tn3926
transposons from E-coli. The specific binding of the Tn3
transposase to DNA has been demonstrated. Sequence
analysis has suggested that the invariant triad of
Asp689, Asp765, Glu895 (numbering as in Tn3) may
correspond to the D-D-35-E motif previously implicated
in the catalysis of numerous transposases.
Length = 968
Score = 24.2 bits (53), Expect = 8.4
Identities = 16/52 (30%), Positives = 21/52 (40%), Gaps = 15/52 (28%)
Query: 5 QAFTFEAAHRLPRVPKTHKCHRMHGHSYRVELVMEGDVDPKTGFVDDFFNIE 56
+A LPRV T EL++E VD TGF D F ++
Sbjct: 564 EALRAALYSMLPRVRLT-------------ELLLE--VDAWTGFSDAFTHLS 600
>gnl|CDD|147088 pfam04754, Transposase_31, Putative transposase, YhgA-like. This
family of putative transposases includes the YhgA
sequence from Escherichia coli and several prokaryotic
homologues.
Length = 250
Score = 24.1 bits (53), Expect = 9.6
Identities = 6/31 (19%), Positives = 10/31 (32%)
Query: 54 NIEQYFSPLLEKLDHHCLNEIEELENPTAEN 84
+ + + +L EEL AE
Sbjct: 215 DTSELEEEFIRELAKRVPEHGEELMMTIAEK 245
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
0.322 0.136 0.430
Gapped
Lambda K H
0.267 0.0797 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 1,554,817
Number of extensions: 74302
Number of successful extensions: 188
Number of sequences better than 10.0: 1
Number of HSP's gapped: 177
Number of HSP's successfully gapped: 21
Length of query: 118
Length of database: 6,263,737
Length adjustment: 81
Effective length of query: 37
Effective length of database: 4,513,408
Effective search space: 166996096
Effective search space used: 166996096
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: 51 (23.3 bits)