RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|255764506|ref|YP_003065297.2| GTP cyclohydrolase I
[Candidatus Liberibacter asiaticus str. psy62]
(205 letters)
>gnl|CDD|30650 COG0302, FolE, GTP cyclohydrolase I [Coenzyme metabolism].
Length = 195
Score = 237 bits (607), Expect = 1e-63
Identities = 92/182 (50%), Positives = 127/182 (69%), Gaps = 3/182 (1%)
Query: 19 EEAKEAIRVILRWIGDDPDREGLKDTPDRVIKSYKELFAGYKQIPTTQDTSRFHFGEASK 78
E + A+R +L +G+DPDREGL +TP RV K+Y+ELF+GY + P F E
Sbjct: 13 ERIEAAVRELLEALGEDPDREGLLETPKRVAKAYRELFSGYDEDPAEIVLEAT-FEEDH- 70
Query: 79 YQDMVLIKDISFFSYCEHHILPIWGKIHLAYIPKKHVIGLSKLVRILEVYSRRLQIQERL 138
+MVL+KDI F+S CEHH+LP +GK H+AYIP VIGLSK+ RI+++++RRLQ+QERL
Sbjct: 71 -DEMVLVKDIEFYSLCEHHLLPFFGKAHVAYIPDGKVIGLSKIARIVDIFARRLQVQERL 129
Query: 139 TMQIAHAIESSTDSKGVAVLIEGQHMCMSMRGIKRDGLTTVTTAFTGEFSRDKGKTDFFL 198
T QIA A++ +GVAV+IE +HMCMSMRG+++ G +TVT+A G F D FL
Sbjct: 130 TEQIADALQEILKPRGVAVVIEAEHMCMSMRGVRKPGSSTVTSALRGLFKEDAKTRAEFL 189
Query: 199 KM 200
++
Sbjct: 190 RL 191
>gnl|CDD|29763 cd00642, GTP_cyclohydro1, GTP cyclohydrolase I (GTP-CH-I) catalyzes
the conversion of GTP into dihydroneopterin
triphosphate. The enzyme product is the precursor of
tetrahydrofolate in eubacteria, fungi, and plants and of
the folate analogs in methanogenic bacteria. In
vertebrates and insects it is the biosynthtic precursor
of tetrahydrobiopterin (BH4) which is involved in the
formation of catacholamines, nitric oxide, and the
stimulation of T lymphocytes. The biosynthetic reaction
of BH4 is controlled by a regulatory protein GFRP which
mediates feedback inhibition of GTP-CH-I by BH4. This
inhibition is reversed by phenylalanine. The decameric
GTP-CH-I forms a complex with two pentameric GFRP in the
presence of phenylalanine or a combination of GTP and
BH4, respectively..
Length = 185
Score = 198 bits (505), Expect = 9e-52
Identities = 92/183 (50%), Positives = 128/183 (69%), Gaps = 3/183 (1%)
Query: 18 VEEAKEAIRVILRWIGDDPDREGLKDTPDRVIKSYKELFAGYKQIPTTQDTSRFHFGEAS 77
+E+ A+R IL +G+DP+REGL +TP+RV K+Y+E+ +GY Q + F E
Sbjct: 3 LEKIAAAVREILELLGEDPNREGLLETPERVAKAYQEITSGYDQALNDPKNTAI-FDE-- 59
Query: 78 KYQDMVLIKDISFFSYCEHHILPIWGKIHLAYIPKKHVIGLSKLVRILEVYSRRLQIQER 137
+ +MV++KDI+ FS CEHH++P +GK+H+AYIPK VIGLSKL RI+E +SRRLQ+QER
Sbjct: 60 DHDEMVIVKDITLFSMCEHHLVPFYGKVHIAYIPKDKVIGLSKLARIVEFFSRRLQVQER 119
Query: 138 LTMQIAHAIESSTDSKGVAVLIEGQHMCMSMRGIKRDGLTTVTTAFTGEFSRDKGKTDFF 197
LT QIA AI+ +GVAV+IE HMCM MRG+++ G TVT+A G F D + F
Sbjct: 120 LTKQIAVAIQEILGPQGVAVVIEATHMCMVMRGVRKPGSKTVTSAMLGVFKEDPKTREEF 179
Query: 198 LKM 200
L++
Sbjct: 180 LRL 182
>gnl|CDD|37909 KOG2698, KOG2698, KOG2698, GTP cyclohydrolase I [Coenzyme transport
and metabolism].
Length = 247
Score = 179 bits (456), Expect = 4e-46
Identities = 82/192 (42%), Positives = 121/192 (63%), Gaps = 5/192 (2%)
Query: 12 KLKKPTVEEAKEAIRVILRWIGDDPDREGLKDTPDRVIKSYKELFAGYKQ-IPTTQDTSR 70
+ + + E A IL+ +G+DP+R+GL TP+R K+ GY+Q + + +
Sbjct: 58 EESEEVLPEMANAYSSILKSLGEDPNRQGLLKTPERAAKAMLYFTKGYEQNLNDVLNEAV 117
Query: 71 FHFGEASKYQDMVLIKDISFFSYCEHHILPIWGKIHLAYIPKKHVIGLSKLVRILEVYSR 130
F + +MV++KDI FS CEHH++P +GK+H+ YIP K V+GLSKL RI+E+YSR
Sbjct: 118 FD----EDHDEMVIVKDIEMFSMCEHHLVPFYGKVHIGYIPNKKVLGLSKLARIVEMYSR 173
Query: 131 RLQIQERLTMQIAHAIESSTDSKGVAVLIEGQHMCMSMRGIKRDGLTTVTTAFTGEFSRD 190
RLQ+QERLT QIA A+ + GVAV++E HMCM MRG+++ G +TVT+ G F D
Sbjct: 174 RLQVQERLTKQIAVALSQAVQPAGVAVVVEATHMCMVMRGVQKIGSSTVTSTMLGVFRDD 233
Query: 191 KGKTDFFLKMTH 202
+ FL + +
Sbjct: 234 PKTREEFLNLIN 245
>gnl|CDD|144718 pfam01227, GTP_cyclohydroI, GTP cyclohydrolase I. This family
includes GTP cyclohydrolase enzymes and a family of
related bacterial proteins.
Length = 86
Score = 142 bits (361), Expect = 6e-35
Identities = 48/86 (55%), Positives = 65/86 (75%)
Query: 100 PIWGKIHLAYIPKKHVIGLSKLVRILEVYSRRLQIQERLTMQIAHAIESSTDSKGVAVLI 159
P +GK H+AYIP VIGLSKL R ++ ++RRLQ+QERLT QIA A+ + KGVAV+I
Sbjct: 1 PFFGKAHIAYIPNGKVIGLSKLARYVDSFARRLQVQERLTNQIADALVEALKPKGVAVVI 60
Query: 160 EGQHMCMSMRGIKRDGLTTVTTAFTG 185
E +H+CM+MRG+++ G TVT+A G
Sbjct: 61 EAEHLCMTMRGVRKPGSKTVTSALRG 86
>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 = 43.2 bits (101), Expect = 6e-05
Identities = 20/120 (16%), Positives = 39/120 (32%), Gaps = 16/120 (13%)
Query: 80 QDMVLIKDISFFSYC----EHHILPIWGKIHLAYIPKKHV----------IGLSKLVRIL 125
D V +KD+ + + ++ + + + R+
Sbjct: 1 TDGVRVKDLLKVTRLGFVTLERTVGQIFEVDVTLSWDGKKAAASDDVATDTVYNTIYRLA 60
Query: 126 EVYSRRLQIQERLTMQIAHAIESSTDSK--GVAVLIEGQHMCMSMRGIKRDGLTTVTTAF 183
+ Y Q+ ERL +IA+ I S V V + H + RG+ + + T
Sbjct: 61 KEYVEGSQLIERLAEEIAYLIAEHFLSSVAEVKVEEKKPHAVIPDRGVFKPTDSPGVTIE 120
>gnl|CDD|31123 COG0780, COG0780, Enzyme related to GTP cyclohydrolase I [General
function prediction only].
Length = 149
Score = 33.7 bits (77), Expect = 0.039
Identities = 11/58 (18%), Positives = 24/58 (41%)
Query: 100 PIWGKIHLAYIPKKHVIGLSKLVRILEVYSRRLQIQERLTMQIAHAIESSTDSKGVAV 157
P + I++ YIP K + L L + E+ +I + +++ + + V
Sbjct: 59 PDFATIYIEYIPDKACVESKSLKLYLFSFRNHGIFHEQCANRIFNDLKALLKPEYLEV 116
>gnl|CDD|31307 COG1110, COG1110, Reverse gyrase [DNA replication, recombination,
and repair].
Length = 1187
Score = 29.1 bits (65), Expect = 0.81
Identities = 20/42 (47%), Positives = 24/42 (57%), Gaps = 1/42 (2%)
Query: 2 KCLRTGVFNMKLKKPTVEEAKE-AIRVILRWIGDDPDREGLK 42
KC R G N++ K TVE +E A+ V IG DPD EG K
Sbjct: 710 KCPRCGSRNVEDKTETVEALRELALEVDEILIGTDPDTEGEK 751
>gnl|CDD|33360 COG3558, COG3558, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 154
Score = 28.5 bits (63), Expect = 1.5
Identities = 19/77 (24%), Positives = 33/77 (42%), Gaps = 7/77 (9%)
Query: 17 TVEEAKEAIRVILR-WIGDDPDREGLKDTPDRVIKSYKELFAGYKQIPTTQDTSRFHFGE 75
T E A + +R+ W DP + L T D ++ E F G ++I F +
Sbjct: 10 TAETAIQKVRMAEDAWNSRDPAKVALAYTEDSFWRNRAEFFQGREKI------QEFLTRK 63
Query: 76 ASKYQDMVLIKDISFFS 92
+ + LIK++ F+
Sbjct: 64 WDRELEYRLIKELWAFT 80
>gnl|CDD|173781 cd03361, TOPRIM_TopoIA_RevGyr, TopoIA_RevGyr : The
topoisomerase-primase (TORPIM) domain found in members
of the type IA family of DNA topoisomerases (Topo IA)
similar to the ATP-dependent reverse gyrase found in
archaea and thermophilic bacteria. Type IA DNA
topoisomerases remove (relax) negative supercoils in the
DNA by: cleaving one strand of the DNA duplex,
covalently linking to the 5' phosphoryl end of the DNA
break and, allowing the other strand of the duplex to
pass through the gap. Reverse gyrase is also able to
insert positive supercoils in the presence of ATP and
negative supercoils in the presence of AMPPNP. The
TOPRIM domain has two conserved motifs, one of which
centers at a conserved glutamate and the other one at
two conserved aspartates (DxD). For topoisomerases the
conserved glutamate is believed to act as a general base
in strand joining and, as a general acid in strand
cleavage. The DXD motif may co-ordinate Mg2+, a cofactor
required for full catalytic function.
Length = 170
Score = 27.3 bits (61), Expect = 3.1
Identities = 18/45 (40%), Positives = 21/45 (46%), Gaps = 7/45 (15%)
Query: 2 KCLRTGVFNMKLKKPTVEE----AKEAIRVILRWIGDDPDREGLK 42
KC R G N+ K T+E A E V+ I DPD EG K
Sbjct: 93 KCPRCGSENIDDKLETLEALRELALEVDEVL---IATDPDTEGEK 134
>gnl|CDD|173783 cd03363, TOPRIM_TopoIA_TopoI, TOPRIM_TopoIA_TopoI: The
topoisomerase-primase (TORPIM) domain found in members
of the type IA family of DNA topoisomerases (Topo IA)
similar to Escherichia coli DNA topoisomerase I. Type
IA DNA topoisomerases remove (relax) negative
supercoils in the DNA by: cleaving one strand of the
DNA duplex, covalently linking to the 5' phosphoryl end
of the DNA break and, allowing the other strand of the
duplex to pass through the gap. The TOPRIM domain has
two conserved motifs, one of which centers at a
conserved glutamate and the other one at two conserved
aspartates (DxD). For topoisomerases the conserved
glutamate is believed to act as a general base in
strand joining and, as a general acid in strand
cleavage. The DXD motif may co-ordinate Mg2+, a
cofactor required for full catalytic function.
Length = 123
Score = 27.1 bits (61), Expect = 3.2
Identities = 14/31 (45%), Positives = 17/31 (54%), Gaps = 7/31 (22%)
Query: 14 KKPTVEE----AKEAIRVILRWIGDDPDREG 40
KK V+E AK+A + L DPDREG
Sbjct: 59 KKKVVKELKKLAKKADEIYL---ATDPDREG 86
>gnl|CDD|29502 cd00801, INT_P4, Bacteriophage P4 integrase. P4-like integrases are
found in temperate bacteriophages, integrative plasmids,
pathogenicity and symbiosis islands, and other mobile
genetic elements. They share the same fold in their
catalytic domain and the overall reaction mechanism with
the superfamily of DNA breaking-rejoining enzymes. The
P4 integrase mediates integrative and excisive
site-specific recombination between two sites, called
attachment sites, located on the phage genome and the
bacterial chromosome. The phage attachment site is often
found adjacent to the integrase gene, while the host
attachment sites are typically situated near tRNA
genes..
Length = 357
Score = 26.8 bits (59), Expect = 4.4
Identities = 7/24 (29%), Positives = 14/24 (58%)
Query: 95 EHHILPIWGKIHLAYIPKKHVIGL 118
E H+LP+ GK + I + ++ +
Sbjct: 101 EKHVLPVLGKKPITEITARDLLDV 124
>gnl|CDD|37737 KOG2526, KOG2526, KOG2526, Predicted aminopeptidases - M20/M25/M40
family [Amino acid transport and metabolism].
Length = 555
Score = 26.9 bits (59), Expect = 4.4
Identities = 14/58 (24%), Positives = 22/58 (37%), Gaps = 4/58 (6%)
Query: 22 KEAIRVILRWIGDDPDREGLKDTPDRVIKSYKELFAGY----KQIPTTQDTSRFHFGE 75
KEA+ L P GL+ + + + K + GY K T D F + +
Sbjct: 439 KEAVDSFLDQFASRPRPAGLQRKDESITSNLKSVLEGYLNVVKSAHTKTDAEFFFYDQ 496
>gnl|CDD|173955 cd08196, DHQS-like1, Dehydroquinate synthase (DHQS)-like. DHQS
catalyzes the conversion of DAHP to DHQ in shikimate
pathway for aromatic compounds synthesis.
Dehydroquinate synthase-like proteins. Dehydroquinate
synthase (DHQS) catalyzes the conversion of
3-deoxy-D-arabino-heptulosonate-7-phosphate (DAHP) to
dehydroquinate (DHQ) in the second step of the shikimate
pathway. This pathway involves seven sequential
enzymatic steps in the conversion of erythrose
4-phosphate and phosphoenolpyruvate into chorismate for
subsequent synthesis of aromatic compounds. The activity
of DHQS requires NAD as cofactor. Proteins of this
family share sequence similarity and functional motifs
with that of dehydroquinate synthase, but the specific
function has not been characterized.
Length = 346
Score = 26.6 bits (59), Expect = 4.6
Identities = 13/37 (35%), Positives = 18/37 (48%), Gaps = 6/37 (16%)
Query: 144 HAIESSTD---SKGVAVLIEGQHMCMSMRGIKRDGLT 177
HA+ES+T+ G+AV G M M+ G T
Sbjct: 231 HALESATNFAIPHGIAV---GLGMLMANTIAVLAGGT 264
>gnl|CDD|37281 KOG2070, KOG2070, KOG2070, Guanine nucleotide exchange factor
[Nucleotide transport and metabolism].
Length = 661
Score = 26.2 bits (57), Expect = 6.9
Identities = 20/71 (28%), Positives = 26/71 (36%), Gaps = 2/71 (2%)
Query: 115 VIGLSKLVRILEVYSRRLQIQERLTMQIAHAIESSTDSKGVAVLIEGQHMCMSMRGIKRD 174
GLSK R L+ Y LQ ER M+ H + +AV C +R K
Sbjct: 230 TTGLSKPFRRLDKYPTLLQELERH-MEDYHPDRGDI-QRSMAVFKNLSAQCQELRKQKEL 287
Query: 175 GLTTVTTAFTG 185
L +T
Sbjct: 288 ELQILTEPIRN 298
>gnl|CDD|35298 KOG0075, KOG0075, KOG0075, GTP-binding ADP-ribosylation factor-like
protein [General function prediction only].
Length = 186
Score = 26.0 bits (57), Expect = 8.3
Identities = 10/34 (29%), Positives = 17/34 (50%), Gaps = 1/34 (2%)
Query: 162 QHMCMSMRGIKRDGLTT-VTTAFTGEFSRDKGKT 194
+ M +S+ G++ G TT V G++ D T
Sbjct: 19 EEMELSLVGLQNSGKTTLVNVIARGQYLEDMIPT 52
>gnl|CDD|99985 cd03814, GT1_like_2, This family is most closely related to the GT1
family of glycosyltransferases. Glycosyltransferases
catalyze the transfer of sugar moieties from activated
donor molecules to specific acceptor molecules, forming
glycosidic bonds. The acceptor molecule can be a lipid,
a protein, a heterocyclic compound, or another
carbohydrate residue. This group of glycosyltransferases
is most closely related to the previously defined
glycosyltransferase family 1 (GT1). The members of this
family may transfer UDP, ADP, GDP, or CMP linked sugars.
The diverse enzymatic activities among members of this
family reflect a wide range of biological functions. The
protein structure available for this family has the GTB
topology, one of the two protein topologies observed for
nucleotide-sugar-dependent glycosyltransferases. GTB
proteins have distinct N- and C- terminal domains each
containing a typical Rossmann fold. The two domains have
high structural homology despite minimal sequence
homology. The large cleft that separates the two domains
includes the catalytic center and permits a high degree
of flexibility. The members of this family are found
mainly in bacteria and eukaryotes..
Length = 364
Score = 26.0 bits (58), Expect = 8.3
Identities = 10/45 (22%), Positives = 14/45 (31%), Gaps = 6/45 (13%)
Query: 17 TVEEAKEAIRVILRWIGDDPDREGLKDTPDRVIKSYKELFAGYKQ 61
+ V L +GD P R L+ V F G+
Sbjct: 218 ADLPLRRRPPVRLVIVGDGPARARLEARYPNVH------FLGFLD 256
>gnl|CDD|147324 pfam05088, Bac_GDH, Bacterial NAD-glutamate dehydrogenase. This
family consists of several bacterial proteins which are
closely related to NAD-glutamate dehydrogenase found in
Streptomyces clavuligerus. Glutamate dehydrogenases
(GDHs) are a broadly distributed group of enzymes that
catalyse the reversible oxidative deamination of
glutamate to ketoglutarate and ammonia.
Length = 1526
Score = 25.9 bits (58), Expect = 8.7
Identities = 14/42 (33%), Positives = 20/42 (47%), Gaps = 2/42 (4%)
Query: 120 KLVRILEVYSRR--LQIQERLTMQIAHAIESSTDSKGVAVLI 159
L+ ILE Y R QI E ++IA I S + V + +
Sbjct: 292 ALLNILETYPRDELFQISEDELLEIAMGILSLQERPRVRLFL 333
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
0.323 0.138 0.407
Gapped
Lambda K H
0.267 0.0826 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 2,468,812
Number of extensions: 125649
Number of successful extensions: 331
Number of sequences better than 10.0: 1
Number of HSP's gapped: 327
Number of HSP's successfully gapped: 28
Length of query: 205
Length of database: 6,263,737
Length adjustment: 89
Effective length of query: 116
Effective length of database: 4,340,536
Effective search space: 503502176
Effective search space used: 503502176
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 55 (24.8 bits)