RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 032873
(131 letters)
>gnl|CDD|178534 PLN02948, PLN02948, phosphoribosylaminoimidazole carboxylase.
Length = 577
Score = 99.0 bits (247), Expect = 3e-25
Identities = 45/115 (39%), Positives = 58/115 (50%), Gaps = 11/115 (9%)
Query: 17 GTIPVLASSNGSATSRRKD--DSSVREPSTVFEEENPNGDSTDAPIVGIIMESDLDLPVM 74
G I V+ S +R +P + + P+VGIIM SD DLP M
Sbjct: 376 GHITVVGPSAAEVEARLDQLLAEESADPDALPK---------GTPLVGIIMGSDSDLPTM 426
Query: 75 NDAARTLSDFGVPYEIKILPPHQNCKEALSYALSAKERGIKIIIVGDGVEAHLSG 129
DAA L FGVPYE+ I+ H+ + SYA SA RG+++II G G AHL G
Sbjct: 427 KDAAEILDSFGVPYEVTIVSAHRTPERMFSYARSAHSRGLQVIIAGAGGAAHLPG 481
>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 = 85.2 bits (212), Expect = 3e-22
Identities = 36/73 (49%), Positives = 48/73 (65%)
Query: 59 PIVGIIMESDLDLPVMNDAARTLSDFGVPYEIKILPPHQNCKEALSYALSAKERGIKIII 118
P VGIIM SD DLP M AA+ L +FG+PYE++++ H+ + YA A+ RGIK+II
Sbjct: 1 PKVGIIMGSDSDLPTMEKAAKVLKEFGIPYEVRVVSAHRTPERLFEYAKEAEARGIKVII 60
Query: 119 VGDGVEAHLSGTL 131
G G AHL G +
Sbjct: 61 AGAGGAAHLPGMV 73
>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 = 84.5 bits (210), Expect = 6e-22
Identities = 37/71 (52%), Positives = 48/71 (67%)
Query: 59 PIVGIIMESDLDLPVMNDAARTLSDFGVPYEIKILPPHQNCKEALSYALSAKERGIKIII 118
P+VGIIM S DLPVM +AA+TL +FG+PYE+ + H+ YA A++RGIK+II
Sbjct: 1 PLVGIIMGSTSDLPVMEEAAKTLEEFGIPYEVGVASAHRTPDRLFEYAKEAEDRGIKVII 60
Query: 119 VGDGVEAHLSG 129
G G AHL G
Sbjct: 61 AGAGGAAHLPG 71
>gnl|CDD|223119 COG0041, PurE, Phosphoribosylcarboxyaminoimidazole (NCAIR) mutase
[Nucleotide transport and metabolism].
Length = 162
Score = 84.6 bits (210), Expect = 7e-22
Identities = 34/73 (46%), Positives = 45/73 (61%)
Query: 57 DAPIVGIIMESDLDLPVMNDAARTLSDFGVPYEIKILPPHQNCKEALSYALSAKERGIKI 116
P VGIIM S D M AA L +FGVPYE++++ H+ ++ YA A+ERG+K+
Sbjct: 1 MPPKVGIIMGSKSDWDTMKKAAEILEEFGVPYEVRVVSAHRTPEKMFEYAEEAEERGVKV 60
Query: 117 IIVGDGVEAHLSG 129
II G G AHL G
Sbjct: 61 IIAGAGGAAHLPG 73
>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 = 79.2 bits (196), Expect = 7e-20
Identities = 37/69 (53%), Positives = 47/69 (68%)
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 DGVEAHLSG 129
G AHL G
Sbjct: 61 AGGAAHLPG 69
>gnl|CDD|224605 COG1691, COG1691, NCAIR mutase (PurE)-related proteins [General
function prediction only].
Length = 254
Score = 30.8 bits (70), Expect = 0.13
Identities = 23/82 (28%), Positives = 36/82 (43%), Gaps = 8/82 (9%)
Query: 50 NPNGDSTDAPIVGIIMESDLDLPVMNDAARTLSDFGVP----YEIKILPPHQNCKEALSY 105
+PN + VG++ DLPV +AA T + GV Y++ + H+ LS
Sbjct: 109 DPNYEPKKGGKVGVLSAGTSDLPVAEEAAVTAEELGVEVQKVYDVGVAGIHR----LLSA 164
Query: 106 ALSAKERGIKIIIVGDGVEAHL 127
K ++IV G+E L
Sbjct: 165 LKRLKIEDADVLIVVAGMEGAL 186
>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 = 27.4 bits (61), Expect = 2.0
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|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 = 27.4 bits (62), Expect = 2.6
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 = 3.0
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 = 3.0
Identities = 9/23 (39%), Positives = 11/23 (47%)
Query: 66 ESDLDLPVMNDAARTLSDFGVPY 88
E+DLD + L GVPY
Sbjct: 143 ENDLDGTDTAEKMTALRVVGVPY 165
>gnl|CDD|224409 COG1492, CobQ, Cobyric acid synthase [Coenzyme metabolism].
Length = 486
Score = 27.2 bits (61), Expect = 3.3
Identities = 12/27 (44%), Positives = 15/27 (55%), Gaps = 4/27 (14%)
Query: 109 AKERGIKIIIVGD----GVEAHLSGTL 131
A+ +I+VGD GV A L GTL
Sbjct: 153 AEIADAPVILVGDIDRGGVFASLYGTL 179
>gnl|CDD|184004 PRK13365, PRK13365, protocatechuate 4,5-dioxygenase subunit beta;
Provisional.
Length = 279
Score = 26.8 bits (59), Expect = 3.4
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|239268 cd02970, PRX_like2, Peroxiredoxin (PRX)-like 2 family; hypothetical
proteins that show sequence similarity to PRXs. Members
of this group contain a CXXC motif, similar to TRX. The
second cysteine in the motif corresponds to the
peroxidatic cysteine of PRX, however, these proteins do
not contain the other two residues of the catalytic
triad of PRX. PRXs confer a protective antioxidant role
in cells through their peroxidase activity in which
hydrogen peroxide, peroxynitrate, and organic
hydroperoxides are reduced and detoxified using reducing
equivalents derived from either thioredoxin,
glutathione, trypanothione and AhpF. TRXs alter the
redox state of target proteins by catalyzing the
reduction of their disulfide bonds via the CXXC motif
using reducing equivalents derived from either NADPH or
ferredoxins.
Length = 149
Score = 26.2 bits (58), Expect = 4.5
Identities = 19/79 (24%), Positives = 26/79 (32%), Gaps = 30/79 (37%)
Query: 68 DLDLPVMNDAARTLSD--------------FGVPYEIKILPPHQNCKEALSYALSA---- 109
D +LP TLS FG P+ C+E L ALS
Sbjct: 4 DFELPDAGGETVTLSALLGEGPVVVVFYRGFGCPF----------CREYLR-ALSKLLPE 52
Query: 110 -KERGIKIIIVGDGVEAHL 127
G++++ VG L
Sbjct: 53 LDALGVELVAVGPESPEKL 71
>gnl|CDD|223840 COG0769, MurE, UDP-N-acetylmuramyl tripeptide synthase [Cell
envelope biogenesis, outer membrane].
Length = 475
Score = 26.5 bits (59), Expect = 5.4
Identities = 21/83 (25%), Positives = 35/83 (42%), Gaps = 10/83 (12%)
Query: 51 PNGDSTDAPIVGIIMESDLDLPVMN-------DAARTLSD--FGVPYEIKILPPHQNCKE 101
+ D + P +G I E D+ ++ D A L+D G+ K + +E
Sbjct: 369 GDRDKSKRPDMGAIAEQLADIVIVTSDNPRSEDPAVILADILAGIEAPEKYEIIE-DREE 427
Query: 102 ALSYALSAKERGIKIIIVGDGVE 124
A+ AL + G ++I G G E
Sbjct: 428 AIRKALDLAKEGDVVLIAGKGHE 450
>gnl|CDD|197223 cd09124, PLDc_like_TrmB_middle, Middle phospholipase D-like domain
of the transcriptional regulator TrmB and similar
proteins. Middle phospholipase D (PLD)-like domain of
the transcriptional regulator TrmB and similar proteins.
TrmB acts as a bifunctional sugar-sensing
transcriptional regulator which controls two operons
encoding maltose/trehalose and maltodextrin ABC
transporters of Pyrococcus fruiosus. It functions as a
dimer. Full length TrmB includes an N-terminal
DNA-binding domain, a C-terminal sugar-binding domain
and middle region that has been named as a PLD-like
domain. The middle domain displays homology to PLD
enzymes, which contain one or two HKD motifs
(H-x-K-x(4)-D, where x represents any amino acid
residue) per chain. The HKD motif characterizes the PLD
superfamily. Due to the lack of key residues related to
PLD activity in the PLD-like domain, members of this
subfamily are unlikely to carry PLD activity.
Length = 126
Score = 25.7 bits (57), Expect = 5.8
Identities = 12/32 (37%), Positives = 18/32 (56%)
Query: 88 YEIKILPPHQNCKEALSYALSAKERGIKIIIV 119
EI I P + +E L A ERG+K++I+
Sbjct: 24 EEIYISLPSEELEELLEELEKAAERGVKVVII 55
>gnl|CDD|236635 PRK09928, PRK09928, choline transport protein BetT; Provisional.
Length = 679
Score = 26.2 bits (58), Expect = 6.0
Identities = 9/29 (31%), Positives = 15/29 (51%)
Query: 72 PVMNDAARTLSDFGVPYEIKILPPHQNCK 100
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 = 7.1
Identities = 13/33 (39%), Positives = 18/33 (54%), Gaps = 4/33 (12%)
Query: 91 KILPPHQNCKEALSYALSAKERGIKIIIVGDGV 123
KI+PP K ++ AL A +G + IVGD
Sbjct: 191 KIVPP----KNGINQALRALHQGEVVGIVGDQA 219
>gnl|CDD|132493 TIGR03452, mycothione_red, mycothione reductase. Mycothiol, a
glutathione analog in Mycobacterium tuberculosis and
related species, can form a disulfide-linked dimer
called mycothione. This enzyme can reduce mycothione to
regenerate two mycothiol molecules. The enzyme shows
some sequence similarity to glutathione-disulfide
reductase, trypanothione-disulfide reductase, and
dihydrolipoamide dehydrogenase. The characterized
protein from M. tuberculosis, a homodimer, has FAD as a
cofactor, one per monomer, and uses NADPH as a
substrate.
Length = 452
Score = 25.9 bits (57), Expect = 7.2
Identities = 15/48 (31%), Positives = 23/48 (47%), Gaps = 8/48 (16%)
Query: 51 PNGDSTDAPIVGIIMESDLDLPVMNDAART-------LSDFGVPYEIK 91
PNGD DA G+ ++ D +++ RT L D PY++K
Sbjct: 265 PNGDLLDAEAAGVEVDED-GRIKVDEYGRTSARGVWALGDVSSPYQLK 311
>gnl|CDD|238245 cd00431, cysteine_hydrolases, Cysteine hydrolases; This family
contains amidohydrolases, like CSHase
(N-carbamoylsarcosine amidohydrolase), involved in
creatine metabolism and nicotinamidase, converting
nicotinamide to nicotinic acid and ammonia in the
pyridine nucleotide cycle. It also contains
isochorismatase, an enzyme that catalyzes the conversion
of isochorismate to 2,3-dihydroxybenzoate and pyruvate,
via the hydrolysis of the vinyl ether bond, and other
related enzymes with unknown function.
Length = 161
Score = 25.7 bits (57), Expect = 7.4
Identities = 6/18 (33%), Positives = 10/18 (55%)
Query: 106 ALSAKERGIKIIIVGDGV 123
A A + G ++I+V D
Sbjct: 128 ARDALDLGYRVIVVEDAC 145
>gnl|CDD|238920 cd01945, ribokinase_group_B, Ribokinase-like subgroup B. Found in
bacteria and plants, this subgroup is part of the
ribokinase/pfkB superfamily. Its oligomerization state
is unknown at this time. .
Length = 284
Score = 25.7 bits (57), Expect = 7.4
Identities = 10/21 (47%), Positives = 12/21 (57%)
Query: 102 ALSYALSAKERGIKIIIVGDG 122
AL A A+ RGI I + DG
Sbjct: 140 ALHLAQEARARGIPIPLDLDG 160
>gnl|CDD|192433 pfam09970, DUF2204, Nucleotidyl transferase of unknown function
(DUF2204). This domain, found in various hypothetical
archaeal proteins, has no known function. However, this
family was identified as belonging to the
nucleotidyltransferase superfamily.
Length = 181
Score = 25.4 bits (56), Expect = 8.6
Identities = 9/25 (36%), Positives = 14/25 (56%), Gaps = 1/25 (4%)
Query: 100 KEALSYALSA-KERGIKIIIVGDGV 123
AL S +ERG+K +++G V
Sbjct: 2 FRALGEVASKLQERGVKFVVIGGTV 26
>gnl|CDD|236417 PRK09224, PRK09224, threonine dehydratase; Reviewed.
Length = 504
Score = 25.5 bits (57), Expect = 9.6
Identities = 9/14 (64%), Positives = 10/14 (71%)
Query: 106 ALSAKERGIKIIIV 119
ALSA GIK +IV
Sbjct: 84 ALSAARLGIKAVIV 97
>gnl|CDD|187744 cd09211, Lumazine_synthase_archaeal, lumazine synthase
(6,7-dimethyl-8-ribityllumazine synthase, LS); catalyzes
the penultimate step in the biosynthesis of riboflavin
(vitamin B2). Archaeal LS is an important enzyme in the
riboflavin biosynthetic pathway. Riboflavin is the
precursor of flavin mononucleotide (FMN) and flavin
adenine dinucleotide (FAD) which are essential cofactors
for the catalysis of a wide range of redox reactions.
These cofactors are also involved in many other
processes involving DNA repair, circadian time-keeping,
light sensing, and bioluminescence. In the final steps
of the riboflavin biosynthetic pathway LS catalyzes the
condensation of the
5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione with
3,4-dihydroxy- 2-butanone-4-phosphate to release water,
inorganic phosphate and 6,7-dimethyl-8-ribityllumazine
(DMRL), and riboflavin synthase (RS) catalyzes a
dismutation of DMRL which yields riboflavin and
5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione. In
the latter reaction, a four-carbon moiety is transferred
between two DMRL molecules serving as donor and
acceptor, respectively. Both the LS and RS catalyzed
reactions are thermodynamically irreversible and can
proceed in the absence of a catalyst. LS from
Methanococcus jannaschii forms capsids with icosahedral
532 symmetry consisting of 60 subunits. Archaeal LSs
share sequence similarity with archaeal RSs, both appear
to have diverged early in the evolution of archaea from
a common ancestor.
Length = 131
Score = 25.0 bits (55), Expect = 9.8
Identities = 22/75 (29%), Positives = 35/75 (46%), Gaps = 11/75 (14%)
Query: 54 DSTDAPIV-GIIM--ESDLDLPVMNDAARTLSD----FGVPYEIKILPPHQNCKEALS-- 104
D DA + G ++ E+ D + N AAR + D +G P + I P + +AL
Sbjct: 54 DDIDAVVTLGAVIKGETKHDELIANQAARKILDLSLEYGKPVTLGISGPGMSRLQALERI 113
Query: 105 --YALSAKERGIKII 117
YA A E +K++
Sbjct: 114 EYYAKRAVEAAVKMV 128
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
0.311 0.130 0.361
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: 6,526,484
Number of extensions: 571332
Number of successful extensions: 637
Number of sequences better than 10.0: 1
Number of HSP's gapped: 636
Number of HSP's successfully gapped: 41
Length of query: 131
Length of database: 10,937,602
Length adjustment: 86
Effective length of query: 45
Effective length of database: 7,123,158
Effective search space: 320542110
Effective search space used: 320542110
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 (21.8 bits)
S2: 53 (24.0 bits)