RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 028883
(202 letters)
>gnl|CDD|130230 TIGR01162, purE, phosphoribosylaminoimidazole carboxylase, PurE
protein. Phosphoribosylaminoimidazole carboxylase is a
fusion protein in plants and fungi, but consists of two
non-interacting proteins in bacteria, PurK and PurE.
This model represents PurK, an N5-CAIR mutase [Purines,
pyrimidines, nucleosides, and nucleotides, Purine
ribonucleotide biosynthesis].
Length = 156
Score = 140 bits (356), Expect = 6e-43
Identities = 66/143 (46%), Positives = 93/143 (65%), Gaps = 1/143 (0%)
Query: 61 VGIIMESDLDLPVMNDAARTLSDFGVPYEIKILPPHQNCKEALSYALSAKERGIKIIIVG 120
VGIIM SD DLP M AA L +FG+PYE++++ H+ + L YA A+ERGIK+II G
Sbjct: 1 VGIIMGSDSDLPTMKKAADILEEFGIPYELRVVSAHRTPELMLEYAKEAEERGIKVIIAG 60
Query: 121 DGVEAHLSGVAAANSQILVIRVPL-LSEDWSEDDVINSIRMPSHVQVASVPRNNAKNAAL 179
G AHL G+ AA + + VI VP+ D +++ ++MPS V VA+V NA NAAL
Sbjct: 61 AGGAAHLPGMVAALTPLPVIGVPVPSKALSGLDSLLSIVQMPSGVPVATVAIGNAGNAAL 120
Query: 180 YAVKVLGIADEDLLERIRKYVEE 202
A ++LGI D +L E++++Y E
Sbjct: 121 LAAQILGIKDPELAEKLKEYREN 143
>gnl|CDD|144362 pfam00731, AIRC, AIR carboxylase. Members of this family catalyze
the decarboxylation of
1-(5-phosphoribosyl)-5-amino-4-imidazole-carboxylate
(AIR). This family catalyze the sixth step of de novo
purine biosynthesis. Some members of this family contain
two copies of this domain.
Length = 150
Score = 139 bits (354), Expect = 1e-42
Identities = 64/145 (44%), Positives = 93/145 (64%), Gaps = 1/145 (0%)
Query: 59 PIVGIIMESDLDLPVMNDAARTLSDFGVPYEIKILPPHQNCKEALSYALSAKERGIKIII 118
P VGIIM SD DLP M AA+ L +FG+PYE++++ H+ + YA A+ RGIK+II
Sbjct: 1 PKVGIIMGSDSDLPTMEKAAKVLKEFGIPYEVRVVSAHRTPERLFEYAKEAEARGIKVII 60
Query: 119 VGDGVEAHLSGVAAANSQILVIRVPLLSEDWS-EDDVINSIRMPSHVQVASVPRNNAKNA 177
G G AHL G+ AA + + VI VP+ S+ D +++ ++MPS + VA+V AKNA
Sbjct: 61 AGAGGAAHLPGMVAALTTLPVIGVPVKSKALGGLDSLLSIVQMPSGIPVATVAIGGAKNA 120
Query: 178 ALYAVKVLGIADEDLLERIRKYVEE 202
AL A ++L + D +L E++ Y EE
Sbjct: 121 ALLAAQILALKDPELAEKLEAYREE 145
>gnl|CDD|223119 COG0041, PurE, Phosphoribosylcarboxyaminoimidazole (NCAIR) mutase
[Nucleotide transport and metabolism].
Length = 162
Score = 137 bits (348), Expect = 1e-41
Identities = 62/147 (42%), Positives = 92/147 (62%), Gaps = 1/147 (0%)
Query: 57 DAPIVGIIMESDLDLPVMNDAARTLSDFGVPYEIKILPPHQNCKEALSYALSAKERGIKI 116
P VGIIM S D M AA L +FGVPYE++++ H+ ++ YA A+ERG+K+
Sbjct: 1 MPPKVGIIMGSKSDWDTMKKAAEILEEFGVPYEVRVVSAHRTPEKMFEYAEEAEERGVKV 60
Query: 117 IIVGDGVEAHLSGVAAANSQILVIRVPLLSEDWS-EDDVINSIRMPSHVQVASVPRNNAK 175
II G G AHL G+ AA + + VI VP+ S+ S D +++ ++MP+ V VA+V NA
Sbjct: 61 IIAGAGGAAHLPGMVAAKTPLPVIGVPVQSKALSGLDSLLSIVQMPAGVPVATVAIGNAA 120
Query: 176 NAALYAVKVLGIADEDLLERIRKYVEE 202
NAAL A ++L I D +L E++ ++ E
Sbjct: 121 NAALLAAQILAIKDPELAEKLAEFREA 147
>gnl|CDD|178534 PLN02948, PLN02948, phosphoribosylaminoimidazole carboxylase.
Length = 577
Score = 145 bits (367), Expect = 8e-41
Identities = 74/189 (39%), Positives = 103/189 (54%), Gaps = 12/189 (6%)
Query: 17 GTIPVLASSNGSATSRRKD--DSSVREPSTVFEEENPNGDSTDAPIVGIIMESDLDLPVM 74
G I V+ S +R +P + + P+VGIIM SD DLP M
Sbjct: 376 GHITVVGPSAAEVEARLDQLLAEESADPDALPK---------GTPLVGIIMGSDSDLPTM 426
Query: 75 NDAARTLSDFGVPYEIKILPPHQNCKEALSYALSAKERGIKIIIVGDGVEAHLSGVAAAN 134
DAA L FGVPYE+ I+ H+ + SYA SA RG+++II G G AHL G+ A+
Sbjct: 427 KDAAEILDSFGVPYEVTIVSAHRTPERMFSYARSAHSRGLQVIIAGAGGAAHLPGMVASM 486
Query: 135 SQILVIRVPLLSEDWSEDDVINSI-RMPSHVQVASVPRNNAKNAALYAVKVLGIADEDLL 193
+ + VI VP+ + D + SI +MP V VA+V NA NA L AV++LG +D DLL
Sbjct: 487 TPLPVIGVPVKTSHLDGLDSLLSIVQMPRGVPVATVAIGNATNAGLLAVRMLGASDPDLL 546
Query: 194 ERIRKYVEE 202
+++ Y E+
Sbjct: 547 DKMEAYQED 555
>gnl|CDD|214965 smart01001, AIRC, AIR carboxylase. Members of this family catalyse
the decarboxylation of
1-(5-phosphoribosyl)-5-amino-4-imidazole-carboxylate
(AIR). This family catalyse the sixth step of de novo
purine biosynthesis. Some members of this family contain
two copies of this domain.
Length = 152
Score = 128 bits (325), Expect = 3e-38
Identities = 61/144 (42%), Positives = 90/144 (62%), Gaps = 3/144 (2%)
Query: 59 PIVGIIMESDLDLPVMNDAARTLSDFGVPYEIKILPPHQNCKEALSYALSAKERGIKIII 118
P+VGIIM S DLPVM +AA+TL +FG+PYE+ + H+ YA A++RGIK+II
Sbjct: 1 PLVGIIMGSTSDLPVMEEAAKTLEEFGIPYEVGVASAHRTPDRLFEYAKEAEDRGIKVII 60
Query: 119 VGDGVEAHLSGVAAANSQILVIRVPLLSEDWS-EDDVINSIRMPSHVQVA--SVPRNNAK 175
G G AHL GV AA + + VI VP+ S D +++ ++MPS + VA ++ + A
Sbjct: 61 AGAGGAAHLPGVVAALTTLPVIGVPVSSGYLGGLDSLLSIVQMPSGIPVATVAIGIDGAF 120
Query: 176 NAALYAVKVLGIADEDLLERIRKY 199
NAAL A ++L + D +L ++ Y
Sbjct: 121 NAALLAAQILALNDPELAAKLAAY 144
>gnl|CDD|224605 COG1691, COG1691, NCAIR mutase (PurE)-related proteins [General
function prediction only].
Length = 254
Score = 37.8 bits (88), Expect = 0.002
Identities = 29/98 (29%), Positives = 43/98 (43%), Gaps = 8/98 (8%)
Query: 50 NPNGDSTDAPIVGIIMESDLDLPVMNDAARTLSDFGVP----YEIKILPPHQNCKEALSY 105
+PN + VG++ DLPV +AA T + GV Y++ + H+ LS
Sbjct: 109 DPNYEPKKGGKVGVLSAGTSDLPVAEEAAVTAEELGVEVQKVYDVGVAGIHR----LLSA 164
Query: 106 ALSAKERGIKIIIVGDGVEAHLSGVAAANSQILVIRVP 143
K ++IV G+E L V A + VI VP
Sbjct: 165 LKRLKIEDADVLIVVAGMEGALPSVVAGLVDVPVIAVP 202
>gnl|CDD|107248 cd01391, Periplasmic_Binding_Protein_Type_1, Type 1 periplasmic
binding fold superfamily. Type 1 periplasmic binding
fold superfamily. This model and hierarchy represent the
ligand binding domains of the LacI family of
transcriptional regulators, periplasmic binding proteins
of the ABC-type transport systems, the family C
G-protein couples receptors (GPCRs), membrane bound
guanylyl cyclases including the family of natriuretic
peptide receptors (NPRs), and the N-terminal
leucine/isoleucine/valine- binding protein (LIVBP)-like
domains of the ionotropic glutamate receptors (iGluRs).
In LacI-like transcriptional regulator and the bacterial
periplasmic binding proteins the ligands are
monosaccharides including lactose, ribose, fructose,
xylose, arabinose, galactose/glucose, and other sugars,
with a few exceptions. Periplasmic sugar binding
proteins are one of the components of ABC transporters
and are involved in the active transport of
water-soluble ligands. The LacI family of proteins
consists of transcriptional regulators related to the
lac repressor. In this case, the sugar binding domain
binds a sugar which changes the DNA binding activity of
the repressor domain. The periplasmic binding proteins
are the primary receptors for chemotaxis and transport
of many sugar based solutes. The core structures of
periplasmic binding proteins are classified into two
types, and they differ in number and order of beta
strands: type 1 has six beta strands, while type 2 has
five beta strands per sub-domain. These two structural
folds are thought to be distantly related via a common
ancestor. Notably, while the N-terminal LIVBP-like
domain of iGluRs belongs to the type 1
periplasmic-binding fold protein superfamily, the
glutamate-binding domain of the iGluR is structurally
similar to the type 2 periplasmic-binding fold.
Length = 269
Score = 30.6 bits (69), Expect = 0.45
Identities = 19/107 (17%), Positives = 38/107 (35%), Gaps = 7/107 (6%)
Query: 77 AARTLSDFGVPYEIKILPPHQNCKEALSYALSAKERGIKIIIVGDGVEAHLSGVAAANSQ 136
+ G E+ + + + AL ++G+ II + L+ V A +
Sbjct: 22 IELAAEEIGRGLEVILADSQSDPERALEALRDLIQQGVDGIIGPPSSSSALAVVELAAAA 81
Query: 137 ILVIRVPLLSEDWSEDDVINSIRMPSHVQVASVPRNNAKNAALYAVK 183
+P++S D + D+ P +V + AA Y +
Sbjct: 82 ----GIPVVSLDATAPDLTGY---PYVFRVGPDNEQAGEAAAEYLAE 121
>gnl|CDD|236259 PRK08401, PRK08401, L-aspartate oxidase; Provisional.
Length = 466
Score = 29.4 bits (66), Expect = 1.3
Identities = 17/62 (27%), Positives = 32/62 (51%), Gaps = 5/62 (8%)
Query: 103 LSYALSAKERGIKIIIVGDGVEAHLSGVAAANSQILVIRVPLLSEDWSEDDVINSIRMPS 162
L+ A+S ++G + I+G G++ S +A A I P+L D V+++IR
Sbjct: 14 LTAAISLAKKGFDVTIIGPGIKKSNSYLAQAG-----IAFPILEGDSIRAHVLDTIRAGK 68
Query: 163 HV 164
++
Sbjct: 69 YI 70
>gnl|CDD|239064 cd02151, NADPH_oxidoreductase_2, NAD(P)H:flavin oxidoreductase-like
family 2. A subfamily of the nitroreductase family
containing uncharacterized proteins that are similar to
nitroreductase. Nitroreductase catalyzes the reduction
of nitroaromatic compounds such as nitrotoluenes,
nitrofurans and nitroimidazoles. This process requires
NAD(P)H as electron donor in an obligatory two-electron
transfer and uses FMN as cofactor. The enzyme is
typically a homodimer. Members of this family are also
called NADH dehydrogenase, oxygen-insensitive NAD(P)H
nitrogenase or dihydropteridine reductase.
Length = 162
Score = 26.5 bits (59), Expect = 6.7
Identities = 16/64 (25%), Positives = 29/64 (45%), Gaps = 10/64 (15%)
Query: 137 ILVIRVPLLSEDWSEDDVINS--IRMPSH--------VQVASVPRNNAKNAALYAVKVLG 186
I+V+ P S+ W ED I + I++ + VQ+ ++ K A Y ++L
Sbjct: 75 IVVVADPRKSDVWIEDASIAAIIIQLTAQDLGLGSCWVQIRGRMHDDGKTAEEYVRRLLN 134
Query: 187 IADE 190
I +
Sbjct: 135 IPEH 138
>gnl|CDD|200477 cd11338, AmyAc_CMD, Alpha amylase catalytic domain found in
cyclomaltodextrinases and related proteins.
Cyclomaltodextrinase (CDase; EC3.2.1.54), neopullulanase
(NPase; EC 3.2.1.135), and maltogenic amylase (MA; EC
3.2.1.133) catalyze the hydrolysis of alpha-(1,4)
glycosidic linkages on a number of substrates including
cyclomaltodextrins (CDs), pullulan, and starch. These
enzymes hydrolyze CDs and starch to maltose and pullulan
to panose by cleavage of alpha-1,4 glycosidic bonds
whereas alpha-amylases essentially lack activity on CDs
and pullulan. They also catalyze transglycosylation of
oligosaccharides to the C3-, C4- or C6-hydroxyl groups
of various acceptor sugar molecules. Since these
proteins are nearly indistinguishable from each other,
they are referred to as cyclomaltodextrinases (CMDs).
The Alpha-amylase family comprises the largest family of
glycoside hydrolases (GH), with the majority of enzymes
acting on starch, glycogen, and related oligo- and
polysaccharides. These proteins catalyze the
transformation of alpha-1,4 and alpha-1,6 glucosidic
linkages with retention of the anomeric center. The
protein is described as having 3 domains: A, B, C. A is
a (beta/alpha) 8-barrel; B is a loop between the beta 3
strand and alpha 3 helix of A; C is the C-terminal
extension characterized by a Greek key. The majority of
the enzymes have an active site cleft found between
domains A and B where a triad of catalytic residues
(Asp, Glu and Asp) performs catalysis. Other members of
this family have lost the catalytic activity as in the
case of the human 4F2hc, or only have 2 residues that
serve as the catalytic nucleophile and the acid/base,
such as Thermus A4 beta-galactosidase with 2 Glu
residues (GH42) and human alpha-galactosidase with 2 Asp
residues (GH31). The family members are quite extensive
and include: alpha amylase, maltosyltransferase,
cyclodextrin glycotransferase, maltogenic amylase,
neopullulanase, isoamylase, 1,4-alpha-D-glucan
maltotetrahydrolase, 4-alpha-glucotransferase,
oligo-1,6-glucosidase, amylosucrase, sucrose
phosphorylase, and amylomaltase.
Length = 389
Score = 27.1 bits (61), Expect = 7.1
Identities = 8/15 (53%), Positives = 12/15 (80%), Gaps = 2/15 (13%)
Query: 109 AKERGIKIIIVGDGV 123
A +RGI++I+ DGV
Sbjct: 112 AHKRGIRVIL--DGV 124
>gnl|CDD|183858 PRK13059, PRK13059, putative lipid kinase; Reviewed.
Length = 295
Score = 26.9 bits (60), Expect = 7.1
Identities = 17/69 (24%), Positives = 30/69 (43%), Gaps = 5/69 (7%)
Query: 53 GDSTDAPIVGIIMESDLDLPVMNDAARTLSDFGVPYEIKILPPHQNCKEALSYALSAKER 112
GD T +V + + ++DLP+ T +DF K L + EA L +K +
Sbjct: 65 GDGTVDNVVNAMKKLNIDLPIGILPVGTANDFA-----KFLGMPTDIGEACEQILKSKPK 119
Query: 113 GIKIIIVGD 121
+ + + D
Sbjct: 120 KVDLGKIND 128
>gnl|CDD|237725 PRK14487, PRK14487, cbb3-type cytochrome c oxidase subunit II;
Provisional.
Length = 217
Score = 26.7 bits (60), Expect = 8.0
Identities = 9/23 (39%), Positives = 11/23 (47%)
Query: 66 ESDLDLPVMNDAARTLSDFGVPY 88
E+DLD + L GVPY
Sbjct: 143 ENDLDGTDTAEKMTALRVVGVPY 165
>gnl|CDD|184004 PRK13365, PRK13365, protocatechuate 4,5-dioxygenase subunit beta;
Provisional.
Length = 279
Score = 26.8 bits (59), Expect = 8.4
Identities = 13/48 (27%), Positives = 24/48 (50%), Gaps = 7/48 (14%)
Query: 86 VPYEIKI----LPPHQNC---KEALSYALSAKERGIKIIIVGDGVEAH 126
VP I + LP + C +AL A+ + +++++VG G +H
Sbjct: 146 VPIAINVLQYPLPTARRCYRLGQALRRAIESYPEDLRVVVVGTGGLSH 193
>gnl|CDD|233074 TIGR00655, PurU, formyltetrahydrofolate deformylase. This model
describes formyltetrahydrofolate deformylases. The
enzyme is a homohexamer. Sequences from a related enzyme
formyl tetrahydrofolate-specific enzyme,
phosphoribosylglycinamide formyltransferase, serve as an
outgroup for phylogenetic analysis. Putative members of
this family, scoring below the trusted cutoff, include a
sequence from Rhodobacter capsulatus that lacks an
otherwise conserved C-terminal region [Purines,
pyrimidines, nucleosides, and nucleotides, Purine
ribonucleotide biosynthesis].
Length = 280
Score = 26.6 bits (59), Expect = 8.9
Identities = 23/68 (33%), Positives = 32/68 (47%), Gaps = 8/68 (11%)
Query: 63 IIMESDLDLPVMNDAARTLS-DFGVPYEIKILPPHQNCKEALSYA---LSAKERGIKIII 118
++ + +DL V+ + LS DF Y KI+ H + A A A ERG+KII
Sbjct: 155 LLKQYQVDLVVLAKYMQILSPDFVKRYPNKIINIHHSFLPAFIGANPYQRAYERGVKII- 213
Query: 119 VGDGVEAH 126
G AH
Sbjct: 214 ---GATAH 218
>gnl|CDD|211334 cd02566, PseudoU_synth_RluE, Pseudouridine synthase, Escherichia
coli RluE. This group is comprised of bacterial
proteins similar to E. coli RluE. Pseudouridine
synthases catalyze the isomerization of specific
uridines in an RNA molecule to pseudouridines
(5-ribosyluracil, psi). No cofactors are required.
Escherichia coli RluE makes psi2457 in 23S RNA. psi2457
is not universally conserved.
Length = 168
Score = 26.2 bits (58), Expect = 9.0
Identities = 11/22 (50%), Positives = 15/22 (68%)
Query: 180 YAVKVLGIADEDLLERIRKYVE 201
Y V+V G+ ED LE++R VE
Sbjct: 70 YYVQVEGVPTEDALEQLRNGVE 91
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
0.313 0.130 0.359
Gapped
Lambda K H
0.267 0.0817 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,311,921
Number of extensions: 970340
Number of successful extensions: 1045
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1036
Number of HSP's successfully gapped: 37
Length of query: 202
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 110
Effective length of database: 6,857,034
Effective search space: 754273740
Effective search space used: 754273740
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 56 (25.2 bits)