RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 031299
(162 letters)
>gnl|CDD|215466 PLN02865, PLN02865, galactokinase.
Length = 423
Score = 254 bits (650), Expect = 1e-84
Identities = 110/161 (68%), Positives = 128/161 (79%), Gaps = 10/161 (6%)
Query: 1 MGEFSWPTEDELKEMRNKVSEMSGRDAEEVRVVVSPYRICPLGAHIDHQGGTVSAMTINK 60
SWP+ +EL E+R +V+ MSGR++ EVRVVVSPYRICPLGAHIDHQGGTVSAMTINK
Sbjct: 1 TCLGSWPSANELDEIRERVAAMSGRNSGEVRVVVSPYRICPLGAHIDHQGGTVSAMTINK 60
Query: 61 GILLGFVPSGDTEVVLRSGQFDGEVRFRIDEIQQPTNSVKKHHAVYASDSAKIKEECKWG 120
GILLGFVPSGD EV+LRS QF+GEVRFR+DEIQ P + S+ KEE WG
Sbjct: 61 GILLGFVPSGDPEVLLRSAQFEGEVRFRVDEIQHPIA----------NVSSDSKEESNWG 110
Query: 121 NYARGALYALQSRGNILTEGIIGYICGSDNLDSSGLSSSAA 161
+YARGA+YALQSRG+ L++GI GYI GS+ LDSSGLSSSAA
Sbjct: 111 DYARGAVYALQSRGHALSQGITGYISGSEGLDSSGLSSSAA 151
>gnl|CDD|223231 COG0153, GalK, Galactokinase [Carbohydrate transport and
metabolism].
Length = 390
Score = 63.9 bits (156), Expect = 1e-12
Identities = 47/153 (30%), Positives = 62/153 (40%), Gaps = 23/153 (15%)
Query: 11 ELKE-MRNKVSEMSGRDAEEVRVVVSPYRICPLGAHIDHQGGTVSAMTINKGILLGFVPS 69
LKE ++ +E G E +P R+ +G H D+ GG V IN G +
Sbjct: 4 SLKEKLQALFAEHFGYV-EPTVTAFAPGRVNLIGEHTDYNGGFVLPCAINYGTYVAVAKR 62
Query: 70 GDTEVVLRSGQFDGEVRFRIDEIQQPTNSVKKHHAVYASDSAKIKEECKWGNYARGALYA 129
D +V L S F D AK K + W NY +G + A
Sbjct: 63 DDGKVRLYSANFG----------------NAGDIFFLLLDIAKEKID-DWANYVKGVIKA 105
Query: 130 LQSRGNILTEGIIGYICGSDNL-DSSGLSSSAA 161
LQ RG T G+ I G N+ +GLSSSAA
Sbjct: 106 LQKRGYAFT-GLDIVISG--NIPIGAGLSSSAA 135
>gnl|CDD|235407 PRK05322, PRK05322, galactokinase; Provisional.
Length = 387
Score = 59.1 bits (144), Expect = 6e-11
Identities = 47/153 (30%), Positives = 67/153 (43%), Gaps = 26/153 (16%)
Query: 12 LKEMRNKVSEMSGRDAEEVRVVVSPYRICPLGAHIDHQGGTVSAMTINKGILLGFVPSGD 71
+E++ K +E+ G +AE V SP RI +G H D+ GG V I G D
Sbjct: 3 KEELKKKFAEVFGEEAE--DVFFSPGRINLIGEHTDYNGGHVFPAAITLGTYGAARKRDD 60
Query: 72 TEVVLRSGQFD--GEVRFRIDEIQQPTNSVKKHHAVYASDSAKIKEECKWGNYARGALYA 129
+V L S F+ G + F +D++ S K W NY +G L
Sbjct: 61 KKVRLYSANFEDLGIIEFDLDDL-----SFDKED--------------DWANYPKGVLKF 101
Query: 130 LQSRGNILTEGIIGYICGSDNL-DSSGLSSSAA 161
LQ G + G I G N+ + +GLSSSA+
Sbjct: 102 LQEAGYKIDHGFDILIYG--NIPNGAGLSSSAS 132
>gnl|CDD|232841 TIGR00131, gal_kin, galactokinase. Galactokinase is a member of
the GHMP kinases (Galactokinase, Homoserine kinase,
Mevalonate kinase, Phosphomevalonate kinase) and shares
with them an amino-terminal domain probably related to
ATP binding.The galactokinases found by This model are
divided into two sets. Prokaryotic forms are generally
shorter. The eukaryotic forms are longer because of
additional central regions and in some cases are known
to be bifunctional, with regulatory activities that are
independent of galactokinase activity [Energy
metabolism, Sugars].
Length = 386
Score = 51.4 bits (123), Expect = 3e-08
Identities = 34/131 (25%), Positives = 48/131 (36%), Gaps = 20/131 (15%)
Query: 32 VVVSPYRICPLGAHIDHQGGTVSAMTINKGILLGFVPSGDTEVVLRSGQFDGEV-RFRID 90
+P R+ +G H D+ G+V I+ G L D V + D + +D
Sbjct: 19 TARAPGRVNLIGEHTDYNDGSVLPCAIDFGTLCAVAVRDDKNVRIYLANADNKFAERSLD 78
Query: 91 EIQQPTNSVKKHHAVYASDSAKIKEECKWGNYARGALYALQSRGNILTEGIIGYICGSDN 150
+ S E W NY +G L+ Q R N G +C +
Sbjct: 79 LP------------LDGS------EVSDWANYFKGVLHVAQERFNSFPLG-ADIVCSGNV 119
Query: 151 LDSSGLSSSAA 161
SGLSSSAA
Sbjct: 120 PTGSGLSSSAA 130
>gnl|CDD|235163 PRK03817, PRK03817, galactokinase; Provisional.
Length = 351
Score = 45.4 bits (108), Expect = 3e-06
Identities = 36/131 (27%), Positives = 56/131 (42%), Gaps = 27/131 (20%)
Query: 32 VVVSPYRICPLGAHIDHQGGTVSAMTINKGILLGFVPSGDTEVVLRSGQFDGEVRFRIDE 91
V SP R+ +G H D+ G V IN L S + + S F+ E F +D+
Sbjct: 2 KVKSPGRVNLIGEHTDYNDGYVLPFAINLYTFLEIEKSE--KFIFYSENFNEEKTFELDK 59
Query: 92 IQQPTNSVKKHHAVYASDSAKIKEECKWGNYARGALYALQSRGNILTEGIIGYICGSDNL 151
+ + NS W +Y +G ++ L+ RG + G+ G + NL
Sbjct: 60 L-EKLNS--------------------WADYIKGVIWVLEKRGYEV-GGVKGKVSS--NL 95
Query: 152 D-SSGLSSSAA 161
+GLSSSA+
Sbjct: 96 PIGAGLSSSAS 106
>gnl|CDD|179937 PRK05101, PRK05101, galactokinase; Provisional.
Length = 382
Score = 41.1 bits (97), Expect = 8e-05
Identities = 34/132 (25%), Positives = 52/132 (39%), Gaps = 23/132 (17%)
Query: 32 VVVSPYRICPLGAHIDHQGGTVSAMTINKGILLGFVPSGDTEVVLRSGQFDGEV-RFRID 90
+ +P R+ +G H D+ G V I+ ++ D V + + +D + F +D
Sbjct: 22 TIQAPGRVNLIGEHTDYNDGFVLPCAIDYQTVISCAKRDDRIVRVIAADYDNQQDEFSLD 81
Query: 91 EIQQPTNSVKKHHAVYASDSAKIKEECKWGNYARGALYALQSRGNILTEGIIGYICGSDN 150
P H E +W NY RG + LQ R G I G N
Sbjct: 82 ---APIV----PH-----------PEQQWANYVRGVVKHLQERNPDFG-GADLVISG--N 120
Query: 151 L-DSSGLSSSAA 161
+ +GLSSSA+
Sbjct: 121 VPQGAGLSSSAS 132
>gnl|CDD|179063 PRK00555, PRK00555, galactokinase; Provisional.
Length = 363
Score = 39.8 bits (93), Expect = 2e-04
Identities = 32/127 (25%), Positives = 49/127 (38%), Gaps = 22/127 (17%)
Query: 35 SPYRICPLGAHIDHQGGTVSAMTINKGILLGFVPSGDTEVVLRSGQFDGEVRFRIDEIQQ 94
+P RI +G H D+ G + + + ++ F P + S + DG R +D
Sbjct: 7 APGRINLIGEHTDYNLGFALPIALPQRTVVTFTPEHTDAITASSDRADGSARIPLDTTPG 66
Query: 95 PTNSVKKHHAVYASDSAKIKEECKWGNYARGALYALQSRGNILTEGIIGYICGSDNLDSS 154
W YA G ++AL+ G+ + G + SD S
Sbjct: 67 QVTG--------------------WAAYAAGVIWALRGAGHPVPGGAMS--ITSDVEIGS 104
Query: 155 GLSSSAA 161
GLSSSAA
Sbjct: 105 GLSSSAA 111
>gnl|CDD|181437 PRK08470, PRK08470, adenylosuccinate lyase; Provisional.
Length = 442
Score = 35.5 bits (82), Expect = 0.007
Identities = 21/62 (33%), Positives = 32/62 (51%), Gaps = 9/62 (14%)
Query: 64 LGFVPSGDTEVVLRSGQFDGEVRFRIDEIQQPTNSVKKHH--AVYASDSAKIKEECKWGN 121
LG +P D E + ++ +FD RIDEI++ T KH A S S + EE ++ +
Sbjct: 37 LGLIPDSDCEKICKNAKFDIA---RIDEIEKTT----KHDLIAFLTSVSESLGEESRFVH 89
Query: 122 YA 123
Y
Sbjct: 90 YG 91
>gnl|CDD|204502 pfam10509, GalKase_gal_bdg, Galactokinase galactose-binding
signature. This is the highly conserved galactokinase
signature sequence which appears to be present in all
galactokinases irrespective of how many other ATP
binding sites, etc that they carry. The function of
this domain appears to be to bind galactose, and the
domain is normally at the N-terminus of the enzymes,
EC:2.7.1.6. This domain is associated with the families
GHMP_kinases_C, pfam08544 and GHMP_kinases_N,
pfam00288.
Length = 52
Score = 32.5 bits (75), Expect = 0.010
Identities = 12/44 (27%), Positives = 17/44 (38%)
Query: 26 DAEEVRVVVSPYRICPLGAHIDHQGGTVSAMTINKGILLGFVPS 69
E V +P R+ +G H D+ GG V IN +
Sbjct: 9 GVEPEGVASAPGRVNLIGEHTDYNGGFVLPAAINLDTYVAVSKR 52
>gnl|CDD|237304 PRK13206, ureC, urease subunit alpha; Reviewed.
Length = 573
Score = 32.0 bits (73), Expect = 0.12
Identities = 18/50 (36%), Positives = 24/50 (48%), Gaps = 1/50 (2%)
Query: 5 SWPTEDELKEMRNKVSEMSGRDAEEVRVVVSPYRICPLGAH-IDHQGGTV 53
+W T +K R + D R V+ Y ICP AH IDH+ G+V
Sbjct: 381 TWQTAHVMKRRRGALPGDGRADNNRARRYVAKYTICPAVAHGIDHEIGSV 430
>gnl|CDD|215285 PLN02521, PLN02521, galactokinase.
Length = 497
Score = 31.6 bits (72), Expect = 0.15
Identities = 39/142 (27%), Positives = 58/142 (40%), Gaps = 40/142 (28%)
Query: 35 SPYRICPLGAHIDHQGGTVSAMTINKGILLGFVPSGDTEVVLRSGQFDGEVRF--RIDEI 92
SP R+ +G HID++G +V M I + DT V +R + ++R D+
Sbjct: 53 SPGRVNLIGEHIDYEGYSVLPMAIRQ----------DTIVAIRRAEGSKKLRIANVNDKY 102
Query: 93 QQPTNSVKKHHAVYASDSAKIKEECKWGNYA----RGALYALQSRG---------NILTE 139
T V D A KWGNY +G L+S+G +++ +
Sbjct: 103 TTCTFPADPDQEV---DLANH----KWGNYFICGYKGVFEFLKSKGVDVGPPVGLDVVVD 155
Query: 140 GIIGYICGSDNLDSSGLSSSAA 161
G + SGLSSSAA
Sbjct: 156 GTVP--------TGSGLSSSAA 169
>gnl|CDD|177574 PHA03278, PHA03278, envelope glycoprotein K; Provisional.
Length = 347
Score = 30.9 bits (70), Expect = 0.23
Identities = 12/60 (20%), Positives = 19/60 (31%), Gaps = 3/60 (5%)
Query: 102 HHAVYAS---DSAKIKEECKWGNYARGALYALQSRGNILTEGIIGYICGSDNLDSSGLSS 158
H VYA + W Y +Y N L IC +D ++ + +
Sbjct: 35 HGCVYAVLPLGELSDGKNFTWEAYNSTLIYVPLGNKNALDFSGFDDICRTDLVNRTAIGG 94
>gnl|CDD|238221 cd00375, Urease_alpha, Urease alpha-subunit; Urease is a
nickel-dependent metalloenzyme that catalyzes the
hydrolysis of urea to form ammonia and carbon dioxide.
Nickel-dependent ureases are found in bacteria, fungi
and plants. Their primary role is to allow the use of
external and internally generated urea as a nitrogen
source. The enzyme consists of 3 subunits, alpha, beta
and gamma, which can be fused and present on a single
protein chain and which in turn forms multimers, mainly
trimers. The large alpha subunit is the catalytic domain
containing an active site with a bi-nickel center
complexed by a carbamylated lysine. The beta and gamma
subunits play a role in subunit association to form the
higher order trimers.
Length = 567
Score = 29.6 bits (67), Expect = 0.73
Identities = 18/51 (35%), Positives = 27/51 (52%), Gaps = 2/51 (3%)
Query: 5 SWPTEDELKEMRNKVSEMSGR-DAEEVRVVVSPYRICPLGAH-IDHQGGTV 53
+W T ++K R + E SG D V+ ++ Y I P AH I H+ G+V
Sbjct: 375 TWQTAHKMKAQRGPLPEDSGDADNFRVKRYIAKYTINPAIAHGISHEVGSV 425
>gnl|CDD|215793 pfam00213, OSCP, ATP synthase delta (OSCP) subunit. The ATP D
subunit from E. coli is the same as the OSCP subunit
which is this family. The ATP D subunit from metazoa are
found in family pfam00401.
Length = 171
Score = 27.5 bits (62), Expect = 2.4
Identities = 13/89 (14%), Positives = 36/89 (40%), Gaps = 35/89 (39%)
Query: 8 TEDELKEMRNKVSEMSGRDAEEVRVVVSPYRICPLGAHIDHQGGTVSAMTINKGILLGFV 67
+E++LK ++ + + +G+ +V++ ++ ++ G V
Sbjct: 114 SEEQLKALKAALEKKTGK---KVKLETK----------------------VDPSLIGGVV 148
Query: 68 PSGDTEVVLRSG--QFDGEVRFRIDEIQQ 94
+R G DG VR +++ +++
Sbjct: 149 --------VRVGDKVIDGSVRGKLERLKR 169
>gnl|CDD|202897 pfam04120, Iron_permease, Low affinity iron permease.
Length = 133
Score = 27.3 bits (61), Expect = 2.8
Identities = 11/38 (28%), Positives = 19/38 (50%)
Query: 8 TEDELKEMRNKVSEMSGRDAEEVRVVVSPYRICPLGAH 45
TE+EL+E+R + ++ E VV + R +G
Sbjct: 96 TEEELEELRAEYERLAEAAWERHDVVHAESREAAIGED 133
>gnl|CDD|234555 TIGR04344, ovoA_Nterm, 5-histidylcysteine sulfoxide synthase.
Ovothiol A is N1-methyl-4-mercaptohistidine. In the
absence of S-adenosylmethione, a methyl donor, the
intermediate produced is 4-mercaptohistidine. In both
Erwinia tasmaniensis and Trypanosoma cruzi, a protein
occurs with 5-histidylcysteine sulfoxide synthase
activity, but these two enzymes and most homologs share
an additional C-terminal methyltransferase domain. Thus
OvoA may be a bifunctional enzyme with
5-histidylcysteine sulfoxide synthase and
4-mercaptohistidine N1-methyltranferase activity. This
model describes the 5-histidylcysteine sulfoxide
synthase domain, a homolog of the ergothioneine
biosynthesis protein EgtB [Biosynthesis of cofactors,
prosthetic groups, and carriers, Glutathione and
analogs].
Length = 442
Score = 27.6 bits (62), Expect = 3.2
Identities = 7/21 (33%), Positives = 12/21 (57%)
Query: 2 GEFSWPTEDELKEMRNKVSEM 22
+ WP+ DE++ R KV +
Sbjct: 100 AHYDWPSVDEVRAYRQKVRAL 120
>gnl|CDD|99857 cd06103, ScCS-like, Saccharomyces cerevisiae (Sc) citrate synthase
(CS)-like. CS catalyzes the condensation of acetyl
coenzyme A (AcCoA) with oxaloacetate (OAA) to form
citrate and coenzyme A (CoA), the first step in the
citric acid cycle (TCA or Krebs cycle). Some CS proteins
function as 2-methylcitrate synthase (2MCS). 2MCS
catalyzes the condensation of propionyl-coenzyme A
(PrCoA) and OAA to form 2-methylcitrate and CoA during
propionate metabolism. The overall CS reaction is
thought to proceed through three partial reactions and
involves both closed and open conformational forms of
the enzyme: a) the carbanion or equivalent is generated
from AcCoA by base abstraction of a proton, b) the
nucleophilic attack of this carbanion on OAA to generate
citryl-CoA, and c) the hydrolysis of citryl-CoA to
produce citrate and CoA. There are two types of CSs:
type I CS and type II CSs. Type I CSs are found in
eukarya, gram-positive bacteria, archaea, and in some
gram-negative bacteria and are homodimers with both
subunits participating in the active site. Type II CSs
are unique to gram-negative bacteria and are
homohexamers of identical subunits (approximated as a
trimer of dimers). This group includes three S.
cerevisiae CS proteins, ScCit1,-2,-3. ScCit1 is a
nuclear-encoded mitochondrial CS with highly specificity
for AcCoA; in addition to having activity with AcCoA, it
plays a part in the construction of the TCA cycle
metabolon. Yeast cells deleted for Cit1 are
hyper-susceptible to apoptosis induced by heat and aging
stress. ScCit2 is a peroxisomal CS involved in the
glyoxylate cycle; in addition to having activity with
AcCoA, it may have activity with PrCoA. ScCit3 is a
mitochondrial CS and functions in the metabolism of
PrCoA; it is a dual specificity CS and 2MCS, having
similar catalytic efficiency with both AcCoA and PrCoA.
The pattern of expression of the ScCIT3 gene follows
that of the ScCIT1 gene and its expression is increased
in the presence of a ScCIT1 deletion. Included in this
group is the Tetrahymena 14 nm filament protein which
functions as a CS in mitochondria and as a cytoskeletal
component in cytoplasm and Geobacter sulfurreducens
(GSu) CS. GSuCS is dimeric and eukaryotic-like; it lacks
2MCS activity and is inhibited by ATP. In contrast to
eukaryotic and other prokaryotic CSs, GSuCIT is not
stimulated by K+ ions. This group contains proteins
which functions exclusively as either a CS or a 2MCS, as
well as those with relaxed specificity which have dual
functions as both a CS and a 2MCS.
Length = 426
Score = 27.6 bits (62), Expect = 3.4
Identities = 15/36 (41%), Positives = 19/36 (52%), Gaps = 4/36 (11%)
Query: 22 MSGRDAEEVRVVVSPYRICPLGAHIDHQGGTVSAMT 57
M G + EE ++ Y L H DH+GG VSA T
Sbjct: 212 MLGYEDEEFTDLMRLY----LTLHSDHEGGNVSAHT 243
>gnl|CDD|153183 cd04911, ACT_AKiii-YclM-BS_1, ACT domains located C-terminal to the
catalytic domain of the lysine plus threonine-sensitive
aspartokinase isoenzyme AKIII. This CD includes the
first of two ACT domains located C-terminal to the
catalytic domain of the lysine plus threonine-sensitive
aspartokinase isoenzyme AKIII, a monofunctional class
enzyme found in Bacilli (Bacillus subtilis (BS) YclM)
and Clostridia species. Aspartokinase is the first
enzyme in the aspartate metabolic pathway and catalyzes
the conversion of aspartate and ATP to aspartylphosphate
and ADP. Bacillus subtilis YclM is reported to be a
single polypeptide of 50 kD. AKIII from Bacillus
subtilis strain 168 is induced by lysine and repressed
by threonine and it is synergistically inhibited by
lysine and threonine. Members of this CD belong to the
superfamily of ACT regulatory domains.
Length = 76
Score = 26.0 bits (58), Expect = 3.9
Identities = 11/42 (26%), Positives = 21/42 (50%), Gaps = 5/42 (11%)
Query: 67 VPSG--DTEVVLRSGQFDGEVRFRI-DEIQQPTN--SVKKHH 103
+PSG D +++R Q E +I EI++ + ++ H
Sbjct: 35 MPSGIDDISIIIRDNQLTDEKEQKILAEIKEELHPDEIEIIH 76
>gnl|CDD|99858 cd06105, ScCit1-2_like, Saccharomyces cerevisiae (Sc) citrate
synthases Cit1-2_like. Citrate synthases (CS) catalyzes
the condensation of acetyl coenzyme A (AcCoA) with
oxaloacetate (OAA) to form citrate and coenzyme A (CoA),
the first step in the citric acid cycle (TCA or Krebs
cycle). Some CS proteins function as 2-methylcitrate
synthase (2MCS). 2MCS catalyzes the condensation of
propionyl-coenzyme A (PrCoA) and OAA to form
2-methylcitrate and CoA during propionate metabolism.
The overall CS reaction is thought to proceed through
three partial reactions and involves both closed and
open conformational forms of the enzyme: a) the
carbanion or equivalent is generated from AcCoA by base
abstraction of a proton, b) the nucleophilic attack of
this carbanion on OAA to generate citryl-CoA, and c) the
hydrolysis of citryl-CoA to produce citrate and CoA.
There are two types of CSs: type I CS and type II CSs.
Type I CSs are found in eukarya, gram-positive bacteria,
archaea, and in some gram-negative bacteria and are
homodimers with both subunits participating in the
active site. Type II CSs are unique to gram-negative
bacteria and are homohexamers of identical subunits
(approximated as a trimer of dimers). ScCit1 is a
nuclear-encoded mitochondrial CS with highly specificity
for AcCoA. In addition to its CS function, ScCit1 plays
a part in the construction of the TCA cycle metabolon.
Yeast cells deleted for Cit1 are hyper-susceptible to
apoptosis induced by heat and aging stress. ScCit2 is a
peroxisomal CS involved in the glyoxylate cycle; in
addition to having activity with AcCoA, it may have
activity with PrCoA. Chicken and pig heart CS, two
Arabidopsis thaliana (Ath) CSs, CSY4 and -5, and
Aspergillus niger (An) CS also belong to this group. Ath
CSY4 has a mitochondrial targeting sequence; AthCSY5 has
no identifiable targeting sequence. AnCS encoded by the
citA gene has both an N-terminal mitochondrial import
signal and a C-terminal peroxisiomal target sequence; it
is not known if both these signals are functional in
vivo. This group contains proteins which functions
exclusively as either a CS or a 2MCS, as well as those
with relaxed specificity which have dual functions as
both a CS and a 2MCS.
Length = 427
Score = 26.9 bits (60), Expect = 4.9
Identities = 9/13 (69%), Positives = 10/13 (76%)
Query: 45 HIDHQGGTVSAMT 57
H DH+GG VSA T
Sbjct: 229 HSDHEGGNVSAHT 241
>gnl|CDD|218701 pfam05698, Trigger_C, Bacterial trigger factor protein (TF)
C-terminus. In the E. coli cytosol, a fraction of the
newly synthesised proteins requires the activity of
molecular chaperones for folding to the native state.
The major chaperones implicated in this folding process
are the ribosome-associated Trigger Factor (TF), and the
DnaK and GroEL chaperones with their respective
co-chaperones. Trigger Factor is an ATP-independent
chaperone and displays chaperone and
peptidyl-prolyl-cis-trans-isomerase (PPIase) activities
in vitro. It is composed of at least three domains, an
N-terminal domain which mediates association with the
large ribosomal subunit, a central substrate binding and
PPIase domain with homology to FKBP proteins, and a
C-terminal domain of unknown function. The positioning
of TF at the peptide exit channel, together with its
ability to interact with nascent chains as short as 57
residues renders TF a prime candidate for being the
first chaperone that binds to the nascent polypeptide
chains. This family represents the C-terminal region of
the protein.
Length = 162
Score = 26.5 bits (59), Expect = 5.2
Identities = 8/25 (32%), Positives = 16/25 (64%)
Query: 7 PTEDELKEMRNKVSEMSGRDAEEVR 31
T++E+KE +++ G + EEV+
Sbjct: 111 VTDEEIKEEIEELASQYGMEPEEVK 135
>gnl|CDD|99859 cd06106, ScCit3_like, Saccharomyces cerevisiae (Sc) 2-methylcitrate
synthase Cit3-like. 2-methylcitrate synthase (2MCS)
catalyzes the condensation of propionyl-coenzyme A
(PrCoA) and oxaloacetate (OAA) to form 2-methylcitrate
and CoA. Citrate synthase (CS) catalyzes the
condensation of acetyl coenzyme A (AcCoA) with OAA to
form citrate and CoA, the first step in the citric acid
cycle (TCA or Krebs cycle). The overall CS reaction is
thought to proceed through three partial reactions and
involves both closed and open conformational forms of
the enzyme: a) the carbanion or equivalent is generated
from AcCoA by base abstraction of a proton, b) the
nucleophilic attack of this carbanion on OAA to generate
citryl-CoA, and c) the hydrolysis of citryl-CoA to
produce citrate and CoA. There are two types of CSs:
type I CS and type II CSs. Type I CSs are found in
eukarya, gram-positive bacteria, archaea, and in some
gram-negative bacteria and are homodimers with both
subunits participating in the active site. Type II CSs
are unique to gram-negative bacteria and are
homohexamers of identical subunits (approximated as a
trimer of dimers). ScCit3 is mitochondrial and functions
in the metabolism of PrCoA; it is a dual specificity CS
and 2MCS, having similar catalytic efficiency with both
AcCoA and PrCoA. The pattern of expression of the ScCIT3
gene follows that of the major mitochondrial CS gene
(CIT1, not included in this group) and its expression is
increased in the presence of a CIT1 deletion. This group
also contains Aspergillus nidulans 2MCS; a deletion of
the gene encoding this protein results in a strain
unable to grow on propionate. This group contains
proteins which functions exclusively as either a CS or a
2MCS, as well as those with relaxed specificity which
have dual functions as both a CS and a 2MCS.
Length = 428
Score = 27.1 bits (60), Expect = 5.6
Identities = 9/16 (56%), Positives = 11/16 (68%)
Query: 42 LGAHIDHQGGTVSAMT 57
+ H DH+GG VSA T
Sbjct: 228 IALHGDHEGGNVSAHT 243
>gnl|CDD|224382 COG1465, COG1465, Predicted alternative 3-dehydroquinate synthase
[Amino acid transport and metabolism].
Length = 376
Score = 26.7 bits (59), Expect = 5.6
Identities = 20/65 (30%), Positives = 29/65 (44%), Gaps = 10/65 (15%)
Query: 10 DELKEMRNKVSEMSGRDAEEVRVVVSPYRICPLGAH----IDHQGGTVSAMTINKGILLG 65
+E+K+ V E E V V+ I PLG+ +D T S MT +G+L+G
Sbjct: 180 EEIKKTAEVVEEAESERLELVTATVT--EIEPLGSGDRVCVD----TCSLMTRGEGMLVG 233
Query: 66 FVPSG 70
G
Sbjct: 234 SQSRG 238
>gnl|CDD|237551 PRK13902, alaS, alanyl-tRNA synthetase; Provisional.
Length = 900
Score = 27.1 bits (61), Expect = 5.7
Identities = 9/29 (31%), Positives = 18/29 (62%)
Query: 10 DELKEMRNKVSEMSGRDAEEVRVVVSPYR 38
++L+ +R KV++ G D EE+ ++ P
Sbjct: 294 EDLRSLRQKVAKKLGIDVEELEELLEPLE 322
>gnl|CDD|236795 PRK10920, PRK10920, putative uroporphyrinogen III
C-methyltransferase; Provisional.
Length = 390
Score = 27.0 bits (60), Expect = 5.8
Identities = 8/21 (38%), Positives = 14/21 (66%)
Query: 8 TEDELKEMRNKVSEMSGRDAE 28
+L E++ KV+ +SG DA+
Sbjct: 111 LAKQLDELQQKVATISGSDAK 131
>gnl|CDD|215844 pfam00296, Bac_luciferase, Luciferase-like monooxygenase.
Length = 252
Score = 26.5 bits (59), Expect = 6.2
Identities = 13/38 (34%), Positives = 18/38 (47%), Gaps = 3/38 (7%)
Query: 6 WPTEDELKEMRNKVSEM---SGRDAEEVRVVVSPYRIC 40
EL E+ ++V +GRD +VRVV S I
Sbjct: 193 GAPPAELAELIDRVRAAAAAAGRDPADVRVVASLPVIV 230
>gnl|CDD|179280 PRK01322, PRK01322, 6-carboxyhexanoate--CoA ligase; Provisional.
Length = 242
Score = 26.4 bits (59), Expect = 6.9
Identities = 14/45 (31%), Positives = 18/45 (40%), Gaps = 2/45 (4%)
Query: 108 SDSAKIKEECKWGNYARGALYALQSRGNILTEGIIGYICGSDNLD 152
KI AL AL S+ I G+I +C SD+ D
Sbjct: 143 RLKEKILLLGLLTERTVDAL-ALASK-VIAHPGVIAELCWSDDPD 185
>gnl|CDD|131387 TIGR02334, prpF, probable AcnD-accessory protein PrpF. The
2-methylcitrate cycle is one of at least five
degradation pathways for propionate via propionyl-CoA.
Degradation of propionate toward pyruvate consumes
oxaloacetate and releases succinate. Oxidation of
succinate back into oxaloacetate by the TCA cycle makes
the 2-methylcitrate pathway a cycle. This family
consists of PrpF, an incompletely characterized protein
that appears to be an essential accessory protein for
the Fe/S-dependent 2-methylisocitrate dehydratase AcnD
(TIGR02333). This protein is related to but distinct
from FldA (part of Pfam family pfam04303), a putative
fluorene degradation protein of Sphingomonas sp. LB126
[Energy metabolism, Fermentation].
Length = 390
Score = 26.3 bits (58), Expect = 8.4
Identities = 13/33 (39%), Positives = 16/33 (48%), Gaps = 3/33 (9%)
Query: 23 SGRDAEEVRVVVSPYRICPLGAHIDHQGGTVSA 55
RD +RV+ SP P G ID GG S+
Sbjct: 35 EARDKLLLRVIGSPD---PYGKQIDGMGGATSS 64
>gnl|CDD|234309 TIGR03683, A-tRNA_syn_arch, alanyl-tRNA synthetase. This family of
alanyl-tRNA synthetases is limited to the archaea, and
is a subset of those sequences identified by the model
pfam07973 covering the second additional domain (SAD) of
alanyl and threonyl tRNA synthetases.
Length = 902
Score = 26.5 bits (59), Expect = 9.0
Identities = 11/31 (35%), Positives = 21/31 (67%)
Query: 8 TEDELKEMRNKVSEMSGRDAEEVRVVVSPYR 38
E++L+E+R KV++ G D EE+ +++P
Sbjct: 296 DEEDLRELRKKVADKIGIDVEELEKIIAPVE 326
>gnl|CDD|188283 TIGR03130, malonate_delta, malonate decarboxylase acyl carrier
protein. Members of this protein family are the acyl
carrier protein, also called the delta subunit, of
malonate decarboxylase. This subunit has the same
covalently bound prosthetic group, derived from and
similar to coenzyme A, as does citrate lyase, although
this protein and the acyl carrier protein of citrate
lyase do not show significant sequence similarity. Both
malonyl and acetyl groups are transferred to the
prosthetic group for catalysis.
Length = 98
Score = 25.3 bits (56), Expect = 9.8
Identities = 11/28 (39%), Positives = 16/28 (57%)
Query: 62 ILLGFVPSGDTEVVLRSGQFDGEVRFRI 89
L+G V SGD EV++ G G+ +I
Sbjct: 19 ALVGVVGSGDLEVLVEPGALGGKTEVQI 46
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
0.315 0.133 0.392
Gapped
Lambda K H
0.267 0.0836 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,111,966
Number of extensions: 726614
Number of successful extensions: 768
Number of sequences better than 10.0: 1
Number of HSP's gapped: 757
Number of HSP's successfully gapped: 42
Length of query: 162
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 73
Effective length of database: 6,990,096
Effective search space: 510277008
Effective search space used: 510277008
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: 55 (24.8 bits)