RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 032570
(138 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 = 130 bits (330), Expect = 7e-40
Identities = 62/139 (44%), Positives = 89/139 (64%), Gaps = 1/139 (0%)
Query: 1 MESDLDLPVMNDAARTLSDFGVPYEIKILPPHQNCKEALSYALSAKERGIKIIIVGDGVE 60
M SD DLP M AA L +FG+PYE++++ H+ + L YA A+ERGIK+II G G
Sbjct: 5 MGSDSDLPTMKKAADILEEFGIPYELRVVSAHRTPELMLEYAKEAEERGIKVIIAGAGGA 64
Query: 61 AHLSGVAAANSQILVIRVPL-LSEDWSEDDVINSIRMPSHVQVASVPRNNAKNAALYAVK 119
AHL G+ AA + + VI VP+ D +++ ++MPS V VA+V NA NAAL A +
Sbjct: 65 AHLPGMVAALTPLPVIGVPVPSKALSGLDSLLSIVQMPSGVPVATVAIGNAGNAALLAAQ 124
Query: 120 VLGIADEDLLERIRKYVEE 138
+LGI D +L E++++Y E
Sbjct: 125 ILGIKDPELAEKLKEYREN 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 = 126 bits (319), Expect = 2e-38
Identities = 59/139 (42%), Positives = 88/139 (63%), Gaps = 1/139 (0%)
Query: 1 MESDLDLPVMNDAARTLSDFGVPYEIKILPPHQNCKEALSYALSAKERGIKIIIVGDGVE 60
M SD DLP M AA+ L +FG+PYE++++ H+ + YA A+ RGIK+II G G
Sbjct: 7 MGSDSDLPTMEKAAKVLKEFGIPYEVRVVSAHRTPERLFEYAKEAEARGIKVIIAGAGGA 66
Query: 61 AHLSGVAAANSQILVIRVPLLSEDWS-EDDVINSIRMPSHVQVASVPRNNAKNAALYAVK 119
AHL G+ AA + + VI VP+ S+ D +++ ++MPS + VA+V AKNAAL A +
Sbjct: 67 AHLPGMVAALTTLPVIGVPVKSKALGGLDSLLSIVQMPSGIPVATVAIGGAKNAALLAAQ 126
Query: 120 VLGIADEDLLERIRKYVEE 138
+L + D +L E++ Y EE
Sbjct: 127 ILALKDPELAEKLEAYREE 145
>gnl|CDD|223119 COG0041, PurE, Phosphoribosylcarboxyaminoimidazole (NCAIR) mutase
[Nucleotide transport and metabolism].
Length = 162
Score = 124 bits (313), Expect = 2e-37
Identities = 57/139 (41%), Positives = 87/139 (62%), Gaps = 1/139 (0%)
Query: 1 MESDLDLPVMNDAARTLSDFGVPYEIKILPPHQNCKEALSYALSAKERGIKIIIVGDGVE 60
M S D M AA L +FGVPYE++++ H+ ++ YA A+ERG+K+II G G
Sbjct: 9 MGSKSDWDTMKKAAEILEEFGVPYEVRVVSAHRTPEKMFEYAEEAEERGVKVIIAGAGGA 68
Query: 61 AHLSGVAAANSQILVIRVPLLSEDWS-EDDVINSIRMPSHVQVASVPRNNAKNAALYAVK 119
AHL G+ AA + + VI VP+ S+ S D +++ ++MP+ V VA+V NA NAAL A +
Sbjct: 69 AHLPGMVAAKTPLPVIGVPVQSKALSGLDSLLSIVQMPAGVPVATVAIGNAANAALLAAQ 128
Query: 120 VLGIADEDLLERIRKYVEE 138
+L I D +L E++ ++ E
Sbjct: 129 ILAIKDPELAEKLAEFREA 147
>gnl|CDD|178534 PLN02948, PLN02948, phosphoribosylaminoimidazole carboxylase.
Length = 577
Score = 128 bits (324), Expect = 8e-36
Identities = 63/139 (45%), Positives = 86/139 (61%), Gaps = 1/139 (0%)
Query: 1 MESDLDLPVMNDAARTLSDFGVPYEIKILPPHQNCKEALSYALSAKERGIKIIIVGDGVE 60
M SD DLP M DAA L FGVPYE+ I+ H+ + SYA SA RG+++II G G
Sbjct: 417 MGSDSDLPTMKDAAEILDSFGVPYEVTIVSAHRTPERMFSYARSAHSRGLQVIIAGAGGA 476
Query: 61 AHLSGVAAANSQILVIRVPLLSEDWSEDDVINSI-RMPSHVQVASVPRNNAKNAALYAVK 119
AHL G+ A+ + + VI VP+ + D + SI +MP V VA+V NA NA L AV+
Sbjct: 477 AHLPGMVASMTPLPVIGVPVKTSHLDGLDSLLSIVQMPRGVPVATVAIGNATNAGLLAVR 536
Query: 120 VLGIADEDLLERIRKYVEE 138
+LG +D DLL+++ Y E+
Sbjct: 537 MLGASDPDLLDKMEAYQED 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 = 115 bits (291), Expect = 5e-34
Identities = 56/138 (40%), Positives = 84/138 (60%), Gaps = 3/138 (2%)
Query: 1 MESDLDLPVMNDAARTLSDFGVPYEIKILPPHQNCKEALSYALSAKERGIKIIIVGDGVE 60
M S DLPVM +AA+TL +FG+PYE+ + H+ YA A++RGIK+II G G
Sbjct: 7 MGSTSDLPVMEEAAKTLEEFGIPYEVGVASAHRTPDRLFEYAKEAEDRGIKVIIAGAGGA 66
Query: 61 AHLSGVAAANSQILVIRVPLLSEDWS-EDDVINSIRMPSHVQVA--SVPRNNAKNAALYA 117
AHL GV AA + + VI VP+ S D +++ ++MPS + VA ++ + A NAAL A
Sbjct: 67 AHLPGVVAALTTLPVIGVPVSSGYLGGLDSLLSIVQMPSGIPVATVAIGIDGAFNAALLA 126
Query: 118 VKVLGIADEDLLERIRKY 135
++L + D +L ++ Y
Sbjct: 127 AQILALNDPELAAKLAAY 144
>gnl|CDD|224605 COG1691, COG1691, NCAIR mutase (PurE)-related proteins [General
function prediction only].
Length = 254
Score = 30.4 bits (69), Expect = 0.20
Identities = 25/78 (32%), Positives = 35/78 (44%), Gaps = 8/78 (10%)
Query: 6 DLPVMNDAARTLSDFGVP----YEIKILPPHQNCKEALSYALSAKERGIKIIIVGDGVEA 61
DLPV +AA T + GV Y++ + H+ LS K ++IV G+E
Sbjct: 129 DLPVAEEAAVTAEELGVEVQKVYDVGVAGIHR----LLSALKRLKIEDADVLIVVAGMEG 184
Query: 62 HLSGVAAANSQILVIRVP 79
L V A + VI VP
Sbjct: 185 ALPSVVAGLVDVPVIAVP 202
>gnl|CDD|236259 PRK08401, PRK08401, L-aspartate oxidase; Provisional.
Length = 466
Score = 29.4 bits (66), Expect = 0.55
Identities = 17/62 (27%), Positives = 32/62 (51%), Gaps = 5/62 (8%)
Query: 39 LSYALSAKERGIKIIIVGDGVEAHLSGVAAANSQILVIRVPLLSEDWSEDDVINSIRMPS 98
L+ A+S ++G + I+G G++ S +A A I P+L D V+++IR
Sbjct: 14 LTAAISLAKKGFDVTIIGPGIKKSNSYLAQAG-----IAFPILEGDSIRAHVLDTIRAGK 68
Query: 99 HV 100
++
Sbjct: 69 YI 70
>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 = 29.1 bits (65), Expect = 0.74
Identities = 19/107 (17%), Positives = 38/107 (35%), Gaps = 7/107 (6%)
Query: 13 AARTLSDFGVPYEIKILPPHQNCKEALSYALSAKERGIKIIIVGDGVEAHLSGVAAANSQ 72
+ G E+ + + + AL ++G+ II + L+ V A +
Sbjct: 22 IELAAEEIGRGLEVILADSQSDPERALEALRDLIQQGVDGIIGPPSSSSALAVVELAAAA 81
Query: 73 ILVIRVPLLSEDWSEDDVINSIRMPSHVQVASVPRNNAKNAALYAVK 119
+P++S D + D+ P +V + AA Y +
Sbjct: 82 ----GIPVVSLDATAPDLTGY---PYVFRVGPDNEQAGEAAAEYLAE 121
>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 = 26.7 bits (60), Expect = 4.3
Identities = 8/15 (53%), Positives = 12/15 (80%), Gaps = 2/15 (13%)
Query: 45 AKERGIKIIIVGDGV 59
A +RGI++I+ DGV
Sbjct: 112 AHKRGIRVIL--DGV 124
>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 = 26.6 bits (59), Expect = 4.5
Identities = 11/22 (50%), Positives = 15/22 (68%)
Query: 116 YAVKVLGIADEDLLERIRKYVE 137
Y V+V G+ ED LE++R VE
Sbjct: 70 YYVQVEGVPTEDALEQLRNGVE 91
>gnl|CDD|237725 PRK14487, PRK14487, cbb3-type cytochrome c oxidase subunit II;
Provisional.
Length = 217
Score = 26.4 bits (59), Expect = 4.9
Identities = 9/23 (39%), Positives = 11/23 (47%)
Query: 2 ESDLDLPVMNDAARTLSDFGVPY 24
E+DLD + L GVPY
Sbjct: 143 ENDLDGTDTAEKMTALRVVGVPY 165
>gnl|CDD|184004 PRK13365, PRK13365, protocatechuate 4,5-dioxygenase subunit beta;
Provisional.
Length = 279
Score = 26.4 bits (58), Expect = 5.5
Identities = 13/48 (27%), Positives = 24/48 (50%), Gaps = 7/48 (14%)
Query: 22 VPYEIKI----LPPHQNC---KEALSYALSAKERGIKIIIVGDGVEAH 62
VP I + LP + C +AL A+ + +++++VG G +H
Sbjct: 146 VPIAINVLQYPLPTARRCYRLGQALRRAIESYPEDLRVVVVGTGGLSH 193
>gnl|CDD|100023 cd06059, Tubulin, The tubulin superfamily includes five distinct
families, the alpha-, beta-, gamma-, delta-, and
epsilon-tubulins and a sixth family (zeta-tubulin) which
is present only in kinetoplastid protozoa. The alpha-
and beta-tubulins are the major components of
microtubules, while gamma-tubulin plays a major role in
the nucleation of microtubule assembly. The delta- and
epsilon-tubulins are widespread but unlike the alpha,
beta, and gamma-tubulins they are not ubiquitous among
eukaryotes. The alpha/beta-tubulin heterodimer is the
structural subunit of microtubules. The alpha- and
beta-tubulins share 40% amino-acid sequence identity,
exist in several isotype forms, and undergo a variety of
posttranslational modifications. The structures of
alpha- and beta-tubulin are basically identical: each
monomer is formed by a core of two beta-sheets
surrounded by alpha-helices. The monomer structure is
very compact, but can be divided into three regions
based on function: the amino-terminal nucleotide-binding
region, an intermediate taxol-binding region and the
carboxy-terminal region which probably constitutes the
binding surface for motor proteins. Also included in
this group is the mitochondrial Misato/DML1 protein
family, involved in mitochondrial fusion and in
mitochondrial distribution and morphology.
Length = 382
Score = 26.5 bits (59), Expect = 5.6
Identities = 16/61 (26%), Positives = 25/61 (40%), Gaps = 10/61 (16%)
Query: 86 SEDDVINSIRMPSHVQV----ASVPRN-NAKNAALYAVKVLGIADE---DLLERIRKYVE 137
+ VIN I ++ V + N +A I E ++L+RIRK VE
Sbjct: 27 LDPRVINEILQGQLSKLFDPNQLVNGKEGSGN--NWARGYYTIGPELIDEILDRIRKQVE 84
Query: 138 E 138
+
Sbjct: 85 K 85
>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 = 26.1 bits (58), Expect = 5.7
Identities = 16/64 (25%), Positives = 29/64 (45%), Gaps = 10/64 (15%)
Query: 73 ILVIRVPLLSEDWSEDDVINS--IRMPSH--------VQVASVPRNNAKNAALYAVKVLG 122
I+V+ P S+ W ED I + I++ + VQ+ ++ K A Y ++L
Sbjct: 75 IVVVADPRKSDVWIEDASIAAIIIQLTAQDLGLGSCWVQIRGRMHDDGKTAEEYVRRLLN 134
Query: 123 IADE 126
I +
Sbjct: 135 IPEH 138
>gnl|CDD|173790 cd04077, Peptidases_S8_PCSK9_ProteinaseK_like, Peptidase S8 family
domain in ProteinaseK-like proteins. The peptidase S8
or Subtilase clan of proteases have a Asp/His/Ser
catalytic triad that is not homologous to trypsin. This
CD contains several members of this clan including:
PCSK9 (Proprotein convertase subtilisin/kexin type 9),
Proteinase_K, Proteinase_T, and other subtilisin-like
serine proteases. PCSK9 posttranslationally regulates
hepatic low-density lipoprotein receptors (LDLRs) by
binding to LDLRs on the cell surface, leading to their
degradation. The binding site of PCSK9 has been
localized to the epidermal growth factor-like repeat A
(EGF-A) domain of the LDLR. Characterized Proteinases K
are secreted endopeptidases with a high degree of
sequence conservation. Proteinases K are not
substrate-specific and function in a wide variety of
species in different pathways. It can hydrolyze keratin
and other proteins with subtilisin-like specificity. The
number of calcium-binding motifs found in these differ.
Proteinase T is a novel proteinase from the fungus
Tritirachium album Limber. The amino acid sequence of
proteinase T as deduced from the nucleotide sequence is
about 56% identical to that of proteinase K.
Length = 255
Score = 26.3 bits (59), Expect = 5.8
Identities = 9/13 (69%), Positives = 9/13 (69%)
Query: 110 AKNAALYAVKVLG 122
AK A L AVKVL
Sbjct: 81 AKKANLVAVKVLD 93
>gnl|CDD|240854 cd12408, RRM_eIF3G_like, RNA recognition motif in eukaryotic
translation initiation factor 3 subunit G (eIF-3G) and
similar proteins. This subfamily corresponds to the RRM
of eIF-3G and similar proteins. eIF-3G, also termed
eIF-3 subunit 4, or eIF-3-delta, or eIF3-p42, or
eIF3-p44, is the RNA-binding subunit of eIF3, a large
multisubunit complex that plays a central role in the
initiation of translation by binding to the 40 S
ribosomal subunit and promoting the binding of
methionyl-tRNAi and mRNA. eIF-3G binds 18 S rRNA and
beta-globin mRNA, and therefore appears to be a
nonspecific RNA-binding protein. eIF-3G is one of the
cytosolic targets and interacts with mature
apoptosis-inducing factor (AIF). eIF-3G contains one RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). This family
also includes yeast eIF3-p33, a homolog of vertebrate
eIF-3G, plays an important role in the initiation phase
of protein synthesis in yeast. It binds both, mRNA and
rRNA, fragments due to an RRM near its C-terminus. .
Length = 77
Score = 24.8 bits (55), Expect = 6.7
Identities = 11/33 (33%), Positives = 16/33 (48%)
Query: 76 IRVPLLSEDWSEDDVINSIRMPSHVQVASVPRN 108
IRV LSED EDD+ R + + ++
Sbjct: 2 IRVTNLSEDADEDDLRELFRPFGPISRVYLAKD 34
>gnl|CDD|236635 PRK09928, PRK09928, choline transport protein BetT; Provisional.
Length = 679
Score = 26.2 bits (58), Expect = 7.1
Identities = 9/29 (31%), Positives = 15/29 (51%)
Query: 8 PVMNDAARTLSDFGVPYEIKILPPHQNCK 36
P M + A+ L G E+ LPP ++ +
Sbjct: 555 PAMEEVAQELRLRGAYVELNELPPEEDER 583
>gnl|CDD|168292 PRK05906, PRK05906, lipid A biosynthesis lauroyl acyltransferase;
Provisional.
Length = 454
Score = 25.9 bits (57), Expect = 8.5
Identities = 13/33 (39%), Positives = 18/33 (54%), Gaps = 4/33 (12%)
Query: 27 KILPPHQNCKEALSYALSAKERGIKIIIVGDGV 59
KI+PP K ++ AL A +G + IVGD
Sbjct: 191 KIVPP----KNGINQALRALHQGEVVGIVGDQA 219
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
0.316 0.133 0.371
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: 7,235,580
Number of extensions: 659062
Number of successful extensions: 1146
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1138
Number of HSP's successfully gapped: 59
Length of query: 138
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 51
Effective length of database: 7,078,804
Effective search space: 361019004
Effective search space used: 361019004
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 (21.6 bits)
S2: 54 (24.4 bits)