RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17692
(211 letters)
>gnl|CDD|133429 cd05293, LDH_1, A subgroup of L-lactate dehydrogenases. L-lactate
dehydrogenases (LDH) are tetrameric enzymes catalyzing
the last step of glycolysis in which pyruvate is
converted to L-lactate. This subgroup is composed of
eukaryotic LDHs. Vertebrate LDHs are non-allosteric.
This is in contrast to some bacterial LDHs that are
activated by an allosteric effector such as
fructose-1,6-bisphosphate. LDHs are part of the
NAD(P)-binding Rossmann fold superfamily, which includes
a wide variety of protein families including the
NAD(P)-binding domains of alcohol dehydrogenases,
tyrosine-dependent oxidoreductases,
glyceraldehyde-3-phosphate dehydrogenases,
formate/glycerate dehydrogenases, siroheme synthases,
6-phosphogluconate dehydrogenases, aminoacid
dehydrogenases, repressor rex, and NAD-binding potassium
channel domains, among others.
Length = 312
Score = 78.4 bits (194), Expect = 2e-17
Identities = 31/49 (63%), Positives = 41/49 (83%)
Query: 109 GHHGIEEEVFLSLPCVMADNGVTHIVNQPLTQEEIEKLKKSAQAIKEVF 157
G HGIE+EVFLSLPC++ +NG+TH++ QPLT+EE EKL+KSA + EV
Sbjct: 262 GLHGIEDEVFLSLPCILGENGITHVIKQPLTEEEQEKLQKSADTLWEVQ 310
Score = 63.4 bits (155), Expect = 4e-12
Identities = 24/39 (61%), Positives = 33/39 (84%)
Query: 154 KEVFLSLPCVMADNGVTHIVNQPLTQEEIEKLKKSAQAI 192
EVFLSLPC++ +NG+TH++ QPLT+EE EKL+KSA +
Sbjct: 268 DEVFLSLPCILGENGITHVIKQPLTEEEQEKLQKSADTL 306
>gnl|CDD|178212 PLN02602, PLN02602, lactate dehydrogenase.
Length = 350
Score = 67.5 bits (165), Expect = 2e-13
Identities = 31/63 (49%), Positives = 41/63 (65%), Gaps = 2/63 (3%)
Query: 96 REQDRRKP-AIHLLGHHGI-EEEVFLSLPCVMADNGVTHIVNQPLTQEEIEKLKKSAQAI 153
R+Q R P ++ G HGI E +VFLSLP + NGV +VN LT EE E+L+KSA+ +
Sbjct: 282 RDQRRIHPVSVLAKGFHGIDEGDVFLSLPAQLGRNGVLGVVNVHLTDEEAERLRKSAKTL 341
Query: 154 KEV 156
EV
Sbjct: 342 WEV 344
Score = 57.5 bits (139), Expect = 6e-10
Identities = 20/38 (52%), Positives = 27/38 (71%)
Query: 155 EVFLSLPCVMADNGVTHIVNQPLTQEEIEKLKKSAQAI 192
+VFLSLP + NGV +VN LT EE E+L+KSA+ +
Sbjct: 304 DVFLSLPAQLGRNGVLGVVNVHLTDEEAERLRKSAKTL 341
>gnl|CDD|233566 TIGR01771, L-LDH-NAD, L-lactate dehydrogenase. This model
represents the NAD-dependent L-lactate dehydrogenases
from bacteria and eukaryotes. This enzyme function as as
the final step in anaerobic glycolysis. Although lactate
dehydrogenases have in some cases been mistaken for
malate dehydrogenases due to the similarity of these two
substrates and the apparent ease with which evolution
can toggle these activities, critical residues have been
identified which can discriminate between the two
activities. At the time of the creation of this model no
hits above the trusted cutoff contained critical
residues typical of malate dehydrogenases [Energy
metabolism, Anaerobic, Energy metabolism,
Glycolysis/gluconeogenesis].
Length = 299
Score = 57.2 bits (139), Expect = 5e-10
Identities = 20/52 (38%), Positives = 35/52 (67%), Gaps = 1/52 (1%)
Query: 104 AIHLLGHHGIEEEVFLSLPCVMADNGVTHIVNQPLTQEEIEKLKKSAQAIKE 155
+ +L G +GI++ V++ +P V+ NGV I+ PL+ EE E +KSA+ +K+
Sbjct: 249 SAYLDGEYGIKD-VYIGVPAVLGRNGVEEIIELPLSDEEKEAFQKSAETLKK 299
Score = 55.3 bits (134), Expect = 3e-09
Identities = 18/41 (43%), Positives = 28/41 (68%)
Query: 153 IKEVFLSLPCVMADNGVTHIVNQPLTQEEIEKLKKSAQAIK 193
IK+V++ +P V+ NGV I+ PL+ EE E +KSA+ +K
Sbjct: 258 IKDVYIGVPAVLGRNGVEEIIELPLSDEEKEAFQKSAETLK 298
>gnl|CDD|133428 cd05292, LDH_2, A subgroup of L-lactate dehydrogenases. L-lactate
dehydrogenases (LDH) are tetrameric enzymes catalyzing
the last step of glycolysis in which pyruvate is
converted to L-lactate. This subgroup is composed
predominantly of bacterial LDHs and a few fungal LDHs.
Bacterial LDHs may be non-allosteric or may be activated
by an allosteric effector such as
fructose-1,6-bisphosphate. LDHs are part of the
NAD(P)-binding Rossmann fold superfamily, which includes
a wide variety of protein families including the
NAD(P)-binding domains of alcohol dehydrogenases,
tyrosine-dependent oxidoreductases,
glyceraldehyde-3-phosphate dehydrogenases,
formate/glycerate dehydrogenases, siroheme synthases,
6-phosphogluconate dehydrogenases, aminoacid
dehydrogenases, repressor rex, and NAD-binding potassium
channel domains, among others.
Length = 308
Score = 55.2 bits (134), Expect = 3e-09
Identities = 23/52 (44%), Positives = 36/52 (69%), Gaps = 1/52 (1%)
Query: 109 GHHGIEEEVFLSLPCVMADNGVTHIVNQPLTQEEIEKLKKSAQAIKEVFLSL 160
G +GI++ V LSLPC++ +GV ++ PL++EE E L+ SA+ +KE SL
Sbjct: 258 GQYGIKD-VALSLPCIVGRSGVERVLPPPLSEEEEEALRASAEVLKEAIESL 308
Score = 50.2 bits (121), Expect = 2e-07
Identities = 19/41 (46%), Positives = 30/41 (73%)
Query: 153 IKEVFLSLPCVMADNGVTHIVNQPLTQEEIEKLKKSAQAIK 193
IK+V LSLPC++ +GV ++ PL++EE E L+ SA+ +K
Sbjct: 262 IKDVALSLPCIVGRSGVERVLPPPLSEEEEEALRASAEVLK 302
>gnl|CDD|133418 cd00300, LDH_like, L-lactate dehydrogenase-like enzymes. Members
of this subfamily are tetrameric NAD-dependent
2-hydroxycarboxylate dehydrogenases including LDHs,
L-2-hydroxyisocaproate dehydrogenases (L-HicDH), and
LDH-like malate dehydrogenases (MDH). Dehydrogenases
catalyze the conversion of carbonyl compounds to
alcohols or amino acids. LDHs catalyze the last step of
glycolysis in which pyruvate is converted to L-lactate.
Vertebrate LDHs are non-allosteric, but some bacterial
LDHs are activated by an allosteric effector such as
fructose-1,6-bisphosphate. L-HicDH catalyzes the
conversion of a variety of 2-oxo carboxylic acids with
medium-sized aliphatic or aromatic side chains. MDH is
one of the key enzymes in the citric acid cycle,
facilitating both the conversion of malate to
oxaloacetate and replenishing levels of oxalacetate by
reductive carboxylation of pyruvate. The LDH-like
subfamily is part of the NAD(P)-binding Rossmann fold
superfamily, which includes a wide variety of protein
families including the NAD(P)-binding domains of alcohol
dehydrogenases, tyrosine-dependent oxidoreductases,
glyceraldehyde-3-phosphate dehydrogenases,
formate/glycerate dehydrogenases, siroheme synthases,
6-phosphogluconate dehydrogenases, aminoacid
dehydrogenases, repressor rex, and NAD-binding potassium
channel domains, among others.
Length = 300
Score = 54.6 bits (132), Expect = 4e-09
Identities = 22/44 (50%), Positives = 31/44 (70%)
Query: 114 EEEVFLSLPCVMADNGVTHIVNQPLTQEEIEKLKKSAQAIKEVF 157
E+V LS+P V+ GV I+ PLT++E KL+KSA+A+KEV
Sbjct: 256 IEDVALSVPAVVGREGVVRILEIPLTEDEEAKLQKSAEALKEVL 299
Score = 51.1 bits (123), Expect = 7e-08
Identities = 20/41 (48%), Positives = 30/41 (73%)
Query: 153 IKEVFLSLPCVMADNGVTHIVNQPLTQEEIEKLKKSAQAIK 193
I++V LS+P V+ GV I+ PLT++E KL+KSA+A+K
Sbjct: 256 IEDVALSVPAVVGREGVVRILEIPLTEDEEAKLQKSAEALK 296
>gnl|CDD|133426 cd05290, LDH_3, A subgroup of L-lactate dehydrogenases. L-lactate
dehydrogenases (LDH) are tetrameric enzymes catalyzing
the last step of glycolysis in which pyruvate is
converted to L-lactate. This subgroup is composed of
some bacterial LDHs from firmicutes,
gammaproteobacteria, and actinobacteria. Vertebrate LDHs
are non-allosteric, but some bacterial LDHs are
activated by an allosteric effector such as
fructose-1,6-bisphosphate. LDHs are part of the
NAD(P)-binding Rossmann fold superfamily, which includes
a wide variety of protein families including the
NAD(P)-binding domains of alcohol dehydrogenases,
tyrosine-dependent oxidoreductases,
glyceraldehyde-3-phosphate dehydrogenases,
formate/glycerate dehydrogenases, siroheme synthases,
6-phosphogluconate dehydrogenase, aminoacid
dehydrogenases, repressor rex, and NAD-binding potassium
channel domains, among others.
Length = 307
Score = 54.6 bits (132), Expect = 4e-09
Identities = 22/50 (44%), Positives = 33/50 (66%), Gaps = 1/50 (2%)
Query: 107 LLGHHGIEEEVFLSLPCVMADNGVTHIVNQPLTQEEIEKLKKSAQAIKEV 156
L G +G+ + V LSLP V+ G+ ++ PL + E+EKL KSA+AI+E
Sbjct: 257 LSGEYGLSD-VALSLPTVIGAKGIERVLEIPLDEWELEKLHKSAKAIRET 305
Score = 51.2 bits (123), Expect = 6e-08
Identities = 24/83 (28%), Positives = 39/83 (46%), Gaps = 9/83 (10%)
Query: 111 HGIEEEVFLSLPCVMADNGVTHIVNQPLTQEEIEKLKKSAQAIKEVFLSLPCVMADNGVT 170
GI + + ++ D V L+ E + +V LSLP V+ G+
Sbjct: 230 AGIAKSASRLIKAILLDERSILPVCTLLSGE---------YGLSDVALSLPTVIGAKGIE 280
Query: 171 HIVNQPLTQEEIEKLKKSAQAIK 193
++ PL + E+EKL KSA+AI+
Sbjct: 281 RVLEIPLDEWELEKLHKSAKAIR 303
>gnl|CDD|133424 cd01339, LDH-like_MDH, L-lactate dehydrogenase-like malate
dehydrogenase proteins. Members of this subfamily have
an LDH-like structure and an MDH enzymatic activity.
Some members, like MJ0490 from Methanococcus jannaschii,
exhibit both MDH and LDH activities. Tetrameric MDHs,
including those from phototrophic bacteria, are more
similar to LDHs than to other MDHs. LDH catalyzes the
last step of glycolysis in which pyruvate is converted
to L-lactate. MDH is one of the key enzymes in the
citric acid cycle, facilitating both the conversion of
malate to oxaloacetate and replenishing levels of
oxalacetate by reductive carboxylation of pyruvate. The
LDH-like MDHs are part of the NAD(P)-binding Rossmann
fold superfamily, which includes a wide variety of
protein families including the NAD(P)-binding domains of
alcohol dehydrogenases, tyrosine-dependent
oxidoreductases, glyceraldehyde-3-phosphate
dehydrogenases, formate/glycerate dehydrogenases,
siroheme synthases, 6-phosphogluconate dehydrogenases,
aminoacid dehydrogenases, repressor rex, and NAD-binding
potassium channel domains, among others.
Length = 300
Score = 54.0 bits (131), Expect = 7e-09
Identities = 20/52 (38%), Positives = 33/52 (63%), Gaps = 1/52 (1%)
Query: 104 AIHLLGHHGIEEEVFLSLPCVMADNGVTHIVNQPLTQEEIEKLKKSAQAIKE 155
+ +L G +GI++ +F+ +P V+ NGV I+ LT EE E KS +++KE
Sbjct: 247 SAYLEGEYGIKD-IFVGVPVVLGKNGVEKIIELDLTDEEKEAFDKSVESVKE 297
Score = 49.4 bits (119), Expect = 3e-07
Identities = 17/41 (41%), Positives = 26/41 (63%)
Query: 153 IKEVFLSLPCVMADNGVTHIVNQPLTQEEIEKLKKSAQAIK 193
IK++F+ +P V+ NGV I+ LT EE E KS +++K
Sbjct: 256 IKDIFVGVPVVLGKNGVEKIIELDLTDEEKEAFDKSVESVK 296
>gnl|CDD|133419 cd00650, LDH_MDH_like, NAD-dependent, lactate dehydrogenase-like,
2-hydroxycarboxylate dehydrogenase family. Members of
this family include ubiquitous enzymes like L-lactate
dehydrogenases (LDH), L-2-hydroxyisocaproate
dehydrogenases, and some malate dehydrogenases (MDH).
LDH catalyzes the last step of glycolysis in which
pyruvate is converted to L-lactate. MDH is one of the
key enzymes in the citric acid cycle, facilitating both
the conversion of malate to oxaloacetate and
replenishing levels of oxalacetate by reductive
carboxylation of pyruvate. The LDH/MDH-like proteins are
part of the NAD(P)-binding Rossmann fold superfamily,
which includes a wide variety of protein families
including the NAD(P)-binding domains of alcohol
dehydrogenases, tyrosine-dependent oxidoreductases,
glyceraldehyde-3-phosphate dehydrogenases,
formate/glycerate dehydrogenases, siroheme synthases,
6-phosphogluconate dehydrogenases, aminoacid
dehydrogenases, repressor rex, and NAD-binding potassium
channel domains, among others.
Length = 263
Score = 52.7 bits (127), Expect = 2e-08
Identities = 20/49 (40%), Positives = 31/49 (63%)
Query: 109 GHHGIEEEVFLSLPCVMADNGVTHIVNQPLTQEEIEKLKKSAQAIKEVF 157
G GI ++V +S+PC++ NGV + LT E+EKL+KSA +K+
Sbjct: 214 GQIGIPDDVVVSVPCIVGKNGVEEPIEVGLTDFELEKLQKSADTLKKEL 262
Score = 47.7 bits (114), Expect = 1e-06
Identities = 20/70 (28%), Positives = 31/70 (44%), Gaps = 8/70 (11%)
Query: 124 VMADNGVTHIVNQPLTQEEIEKLKKSAQAIKEVFLSLPCVMADNGVTHIVNQPLTQEEIE 183
++ D G V +V +S+PC++ NGV + LT E+E
Sbjct: 198 LLNDEGEILPVGVRN--------NGQIGIPDDVVVSVPCIVGKNGVEEPIEVGLTDFELE 249
Query: 184 KLKKSAQAIK 193
KL+KSA +K
Sbjct: 250 KLQKSADTLK 259
>gnl|CDD|133427 cd05291, HicDH_like, L-2-hydroxyisocapronate dehydrogenases and
some bacterial L-lactate dehydrogenases.
L-2-hydroxyisocapronate dehydrogenase (HicDH) catalyzes
the conversion of a variety of 2-oxo carboxylic acids
with medium-sized aliphatic or aromatic side chains.
This subfamily is composed of HicDHs and some bacterial
L-lactate dehydrogenases (LDH). LDHs catalyze the last
step of glycolysis in which pyruvate is converted to
L-lactate. Bacterial LDHs can be non-allosteric or may
be activated by an allosteric effector such as
fructose-1,6-bisphosphate. Members of this subfamily
with known structures such as the HicDH of Lactobacillus
confusus, the non-allosteric LDH of Lactobacillus
pentosus, and the allosteric LDH of Bacillus
stearothermophilus, show that they exist as
homotetramers. The HicDH-like subfamily is part of the
NAD(P)-binding Rossmann fold superfamily, which includes
a wide variety of protein families including the
NAD(P)-binding domains of alcohol dehydrogenases,
tyrosine-dependent oxidoreductases,
glyceraldehyde-3-phosphate dehydrogenases,
formate/glycerate dehydrogenases, siroheme synthases,
6-phosphogluconate dehydrogenases, aminoacid
dehydrogenases, repressor rex, and NAD-binding potassium
channel domains, among others.
Length = 306
Score = 51.3 bits (124), Expect = 6e-08
Identities = 18/44 (40%), Positives = 29/44 (65%)
Query: 114 EEEVFLSLPCVMADNGVTHIVNQPLTQEEIEKLKKSAQAIKEVF 157
E++V++ +P ++ NGV ++ LT+EE EK +KSA IKE
Sbjct: 261 EKDVYIGVPAIIGRNGVEEVIELDLTEEEQEKFEKSADIIKENI 304
Score = 48.6 bits (117), Expect = 4e-07
Identities = 17/41 (41%), Positives = 27/41 (65%)
Query: 153 IKEVFLSLPCVMADNGVTHIVNQPLTQEEIEKLKKSAQAIK 193
K+V++ +P ++ NGV ++ LT+EE EK +KSA IK
Sbjct: 261 EKDVYIGVPAIIGRNGVEEVIELDLTEEEQEKFEKSADIIK 301
>gnl|CDD|223117 COG0039, Mdh, Malate/lactate dehydrogenases [Energy production and
conversion].
Length = 313
Score = 48.7 bits (117), Expect = 5e-07
Identities = 20/52 (38%), Positives = 35/52 (67%), Gaps = 1/52 (1%)
Query: 104 AIHLLGHHGIEEEVFLSLPCVMADNGVTHIVNQPLTQEEIEKLKKSAQAIKE 155
+++L G +G+E+ V+ +P V+ NGV I+ L+ +E EKL KSA+ +K+
Sbjct: 252 SVYLDGEYGVED-VYFGVPAVLGKNGVEEILELLLSDDEQEKLDKSAEELKK 302
Score = 44.9 bits (107), Expect = 9e-06
Identities = 16/41 (39%), Positives = 27/41 (65%)
Query: 153 IKEVFLSLPCVMADNGVTHIVNQPLTQEEIEKLKKSAQAIK 193
+++V+ +P V+ NGV I+ L+ +E EKL KSA+ +K
Sbjct: 261 VEDVYFGVPAVLGKNGVEEILELLLSDDEQEKLDKSAEELK 301
>gnl|CDD|178836 PRK00066, ldh, L-lactate dehydrogenase; Reviewed.
Length = 315
Score = 48.3 bits (116), Expect = 6e-07
Identities = 20/51 (39%), Positives = 32/51 (62%), Gaps = 1/51 (1%)
Query: 106 HLLGHHGIEEEVFLSLPCVMADNGVTHIVNQPLTQEEIEKLKKSAQAIKEV 156
+L G +G EE+V++ +P V+ NG+ IV PL +E +K SA +KE+
Sbjct: 260 YLEGQYG-EEDVYIGVPAVVNRNGIREIVELPLNDDEKQKFAHSADVLKEI 309
Score = 43.3 bits (103), Expect = 3e-05
Identities = 14/41 (34%), Positives = 24/41 (58%)
Query: 153 IKEVFLSLPCVMADNGVTHIVNQPLTQEEIEKLKKSAQAIK 193
++V++ +P V+ NG+ IV PL +E +K SA +K
Sbjct: 267 EEDVYIGVPAVVNRNGIREIVELPLNDDEKQKFAHSADVLK 307
>gnl|CDD|233562 TIGR01763, MalateDH_bact, malate dehydrogenase, NAD-dependent.
This enzyme converts malate into oxaloacetate in the
citric acid cycle. The critical residues which
discriminate malate dehydrogenase from lactate
dehydrogenase have been characterized , and have been
used to set the cutoffs for this model. Sequences
showing [aflimv][ap]R[rk]pgM[st] and [ltv][ilm]gGhgd
were kept above trusted, while those in which the
capitalized residues in the patterns were found to be Q,
E and E were kept below the noise cutoff. Some sequences
in the grey zone have been annotated as malate
dehydrogenases, but none have been characterized.
Phylogenetically, a clade of sequences from eukaryotes
such as Toxoplasma and Plasmodium which include a
characterized lactate dehydrogenase and show abiguous
critical residue patterns appears to be more closely
related to these bacterial sequences than other
eukaryotic sequences. These are relatively long branch
and have been excluded from the model. All other
sequences falling below trusted appear to be
phylogenetically outside of the clade including the
trusted hits. The annotation of Botryococcus braunii as
lactate dehydrogenase appears top be in error. This was
initially annotated as MDH by Swiss-Prot and then
changed. The rationale for either of these annotations
is not traceable [Energy metabolism, TCA cycle].
Length = 305
Score = 48.3 bits (115), Expect = 8e-07
Identities = 21/62 (33%), Positives = 36/62 (58%), Gaps = 4/62 (6%)
Query: 98 QDRRK---PAIHLLGHHGIEEEVFLSLPCVMADNGVTHIVNQPLTQEEIEKLKKSAQAIK 154
+DR++ A +L G +GI+ +++ +P ++ NGV HI L Q E+ L KSA+ +
Sbjct: 241 KDRKRVLPCAAYLDGQYGIDG-IYVGVPVILGKNGVEHIYELKLDQSELALLNKSAKIVD 299
Query: 155 EV 156
E
Sbjct: 300 EN 301
Score = 40.6 bits (95), Expect = 3e-04
Identities = 14/41 (34%), Positives = 23/41 (56%)
Query: 153 IKEVFLSLPCVMADNGVTHIVNQPLTQEEIEKLKKSAQAIK 193
I +++ +P ++ NGV HI L Q E+ L KSA+ +
Sbjct: 259 IDGIYVGVPVILGKNGVEHIYELKLDQSELALLNKSAKIVD 299
>gnl|CDD|180477 PRK06223, PRK06223, malate dehydrogenase; Reviewed.
Length = 307
Score = 47.4 bits (114), Expect = 1e-06
Identities = 18/62 (29%), Positives = 35/62 (56%), Gaps = 4/62 (6%)
Query: 98 QDRRK--PAIHLL-GHHGIEEEVFLSLPCVMADNGVTHIVNQPLTQEEIEKLKKSAQAIK 154
+D+++ P L G +G+++ V++ +P + NGV I+ L EE KS +A+K
Sbjct: 242 KDKKRVLPCSAYLEGEYGVKD-VYVGVPVKLGKNGVEKIIELELDDEEKAAFDKSVEAVK 300
Query: 155 EV 156
++
Sbjct: 301 KL 302
Score = 43.6 bits (104), Expect = 3e-05
Identities = 14/41 (34%), Positives = 23/41 (56%)
Query: 153 IKEVFLSLPCVMADNGVTHIVNQPLTQEEIEKLKKSAQAIK 193
+K+V++ +P + NGV I+ L EE KS +A+K
Sbjct: 260 VKDVYVGVPVKLGKNGVEKIIELELDDEEKAAFDKSVEAVK 300
>gnl|CDD|202437 pfam02866, Ldh_1_C, lactate/malate dehydrogenase, alpha/beta
C-terminal domain. L-lactate dehydrogenases are
metabolic enzymes which catalyze the conversion of
L-lactate to pyruvate, the last step in anaerobic
glycolysis. L-2-hydroxyisocaproate dehydrogenases are
also members of the family. Malate dehydrogenases
catalyze the interconversion of malate to oxaloacetate.
The enzyme participates in the citric acid cycle.
L-lactate dehydrogenase is also found as a lens
crystallin in bird and crocodile eyes.
Length = 173
Score = 39.2 bits (92), Expect = 5e-04
Identities = 18/50 (36%), Positives = 31/50 (62%), Gaps = 1/50 (2%)
Query: 109 GHHGIEEEVFLSLPCVMADNGVTHIVNQ-PLTQEEIEKLKKSAQAIKEVF 157
G++G ++++ S+P V+ +GV +V PL E EKL+KSA +K+
Sbjct: 117 GYYGSPDDIYFSVPVVLGKDGVEKVVEILPLNDFEREKLEKSAAELKKEI 166
Score = 33.1 bits (76), Expect = 0.049
Identities = 16/39 (41%), Positives = 24/39 (61%), Gaps = 1/39 (2%)
Query: 156 VFLSLPCVMADNGVTHIVNQ-PLTQEEIEKLKKSAQAIK 193
++ S+P V+ +GV +V PL E EKL+KSA +K
Sbjct: 125 IYFSVPVVLGKDGVEKVVEILPLNDFEREKLEKSAAELK 163
>gnl|CDD|173376 PTZ00082, PTZ00082, L-lactate dehydrogenase; Provisional.
Length = 321
Score = 38.1 bits (89), Expect = 0.002
Identities = 17/53 (32%), Positives = 26/53 (49%), Gaps = 4/53 (7%)
Query: 109 GHHGIEEEVFLSLPCVMADNGVTHIVNQPLTQEEIEKLKKSAQAIKEVFLSLP 161
GH I ++ P V+ NGV I+ LT EE +K +S + +K + L
Sbjct: 273 GHKDI----YMGTPAVIGANGVEKIIELDLTPEEQKKFDESIKEVKRLEALLK 321
Score = 35.0 bits (81), Expect = 0.016
Identities = 14/40 (35%), Positives = 24/40 (60%)
Query: 154 KEVFLSLPCVMADNGVTHIVNQPLTQEEIEKLKKSAQAIK 193
K++++ P V+ NGV I+ LT EE +K +S + +K
Sbjct: 275 KDIYMGTPAVIGANGVEKIIELDLTPEEQKKFDESIKEVK 314
>gnl|CDD|173409 PTZ00117, PTZ00117, malate dehydrogenase; Provisional.
Length = 319
Score = 33.2 bits (76), Expect = 0.082
Identities = 14/54 (25%), Positives = 30/54 (55%), Gaps = 1/54 (1%)
Query: 104 AIHLLGHHGIEEEVFLSLPCVMADNGVTHIVNQPLTQEEIEKLKKSAQAIKEVF 157
+++L G + + +F+ +P V+ G+ ++ L EE E KS ++I+E+
Sbjct: 259 SVYLNGQYNCKN-LFVGVPVVIGGKGIEKVIELELNAEEKELFDKSIESIQELT 311
Score = 29.3 bits (66), Expect = 1.2
Identities = 12/40 (30%), Positives = 22/40 (55%)
Query: 154 KEVFLSLPCVMADNGVTHIVNQPLTQEEIEKLKKSAQAIK 193
K +F+ +P V+ G+ ++ L EE E KS ++I+
Sbjct: 269 KNLFVGVPVVIGGKGIEKVIELELNAEEKELFDKSIESIQ 308
>gnl|CDD|224192 COG1273, COG1273, Ku-homolog [Replication, recombination, and
repair].
Length = 278
Score = 32.7 bits (75), Expect = 0.095
Identities = 10/32 (31%), Positives = 16/32 (50%), Gaps = 1/32 (3%)
Query: 177 LTQEEIEKLK-KSAQAIKIRDFVKCQVCGKVY 207
L EE+E + +S + I+I FV +Y
Sbjct: 76 LEDEELESVPLESTKTIEIEAFVPRDEIDPIY 107
>gnl|CDD|217143 pfam02614, UxaC, Glucuronate isomerase. This is a family of
Glucuronate isomerases also known as D-glucuronate
isomerase, uronic isomerase, uronate isomerase, or
uronic acid isomerase, EC:5.3.1.12. This enzyme
catalyzes the reactions: D-glucuronate <=>
D-fructuronate and D-galacturonate <=> D-tagaturonate.
It is not however clear where the experimental evidence
for this functional assignment came from and thus this
family has no literature reference.
Length = 469
Score = 32.2 bits (74), Expect = 0.16
Identities = 18/71 (25%), Positives = 29/71 (40%), Gaps = 21/71 (29%)
Query: 116 EVFLSLPCVMADNGVTHIVNQPLTQEEIEKLKKSAQAIKEVFLSLPCVMADNGVTHIVNQ 175
+ F L C +D+G+ +V ++EE + + A + +
Sbjct: 226 DFFHELGCRASDHGLDTVVYAEASEEEADAIFAKALS---------------------GE 264
Query: 176 PLTQEEIEKLK 186
PLT EEIEK K
Sbjct: 265 PLTPEEIEKFK 275
>gnl|CDD|130820 TIGR01759, MalateDH-SF1, malate dehydrogenase. This model
represents a family of malate dehydrogenases in bacteria
and eukaryotes which utilize either NAD or NADP
depending on the species and context. MDH interconverts
malate and oxaloacetate and is a part of the citric acid
cycle as well as the C4 cycle in certain photosynthetic
organisms.
Length = 323
Score = 31.5 bits (72), Expect = 0.26
Identities = 13/47 (27%), Positives = 18/47 (38%), Gaps = 1/47 (2%)
Query: 110 HHGIEEEVFLSLPCVMADNGVTHIV-NQPLTQEEIEKLKKSAQAIKE 155
+GI E + S P +G IV PL KL + + E
Sbjct: 272 PYGIPEGIIFSFPVTCKGDGEWEIVEGLPLDDFVRGKLDATEDELLE 318
>gnl|CDD|133430 cd05294, LDH-like_MDH_nadp, A lactate dehydrogenases-like structure
with malate dehydrogenase enzymatic activity. The
LDH-like MDH proteins have a lactate
dehyhydrogenase-like (LDH-like) structure and malate
dehydrogenase (MDH) enzymatic activity. This subgroup is
composed of some archaeal LDH-like MDHs that prefer
NADP(H) rather than NAD(H) as a cofactor. One member,
MJ0490 from Methanococcus jannaschii, has been observed
to form dimers and tetramers during crystalization,
although it is believed to exist primarilly as a
tetramer in solution. In addition to its MDH activity,
MJ0490 also possesses
fructose-1,6-bisphosphate-activated LDH activity.
Members of this subgroup have a higher sequence
similarity to LDHs than to other MDHs. LDH catalyzes the
last step of glycolysis in which pyruvate is converted
to L-lactate. MDH is one of the key enzymes in the
citric acid cycle, facilitating both the conversion of
malate to oxaloacetate and replenishing levels of
oxalacetate by reductive carboxylation of pyruvate. The
LDH-like MDHs are part of the NAD(P)-binding Rossmann
fold superfamily, which includes a wide variety of
protein families including the NAD(P)- binding domains
of alcohol dehydrogenases, tyrosine-dependent
oxidoreductases, glyceraldehyde-3-phosphate
dehydrogenases, formate/glycerate dehydrogenases,
siroheme synthases, 6-phosphogluconate dehydrogenase,
aminoacid dehydrogenases, repressor rex, and NAD-binding
potassium channel domains, among others.
Length = 309
Score = 31.6 bits (72), Expect = 0.28
Identities = 13/41 (31%), Positives = 24/41 (58%)
Query: 153 IKEVFLSLPCVMADNGVTHIVNQPLTQEEIEKLKKSAQAIK 193
I++V + +P + NG+ IV + +E E +KSA+ +K
Sbjct: 263 IRDVCIGVPVKLGKNGIEEIVPIEMDDDEREAFRKSAEIVK 303
Score = 30.1 bits (68), Expect = 0.82
Identities = 14/44 (31%), Positives = 25/44 (56%), Gaps = 1/44 (2%)
Query: 112 GIEEEVFLSLPCVMADNGVTHIVNQPLTQEEIEKLKKSAQAIKE 155
GI + V + +P + NG+ IV + +E E +KSA+ +K+
Sbjct: 262 GIRD-VCIGVPVKLGKNGIEEIVPIEMDDDEREAFRKSAEIVKK 304
>gnl|CDD|238408 cd00789, KU_like, Ku-core domain, Ku-like subfamily; composed of
prokaryotic homologs of the eukaryotic DNA binding
protein Ku. The alignment includes the core domain
shared by the prokaryotic YkoV-like proteins and the
eukaryotic Ku70 and Ku80. The prokaryotic Ku homologs
are predicted to form homodimers. It is proposed that
the Ku homologs are functionally associated with
ATP-dependent DNA ligase and the eukaryotic-type
primase, probably as components of a double-strand break
repair system.
Length = 256
Score = 30.2 bits (69), Expect = 0.60
Identities = 12/27 (44%), Positives = 16/27 (59%), Gaps = 1/27 (3%)
Query: 176 PLTQEEIEKLK-KSAQAIKIRDFVKCQ 201
LT EE+E L +S + I+I DFV
Sbjct: 72 ILTDEELEALPPESTRTIEIVDFVPLD 98
>gnl|CDD|223918 COG0849, ftsA, Cell division ATPase FtsA [Cell division and
chromosome partitioning].
Length = 418
Score = 30.3 bits (69), Expect = 0.68
Identities = 23/80 (28%), Positives = 39/80 (48%), Gaps = 12/80 (15%)
Query: 127 DNGVTHIVNQPLTQEEIEKLKKSAQA-----IKEVFLSLPC----VMADNGVTHIVN-QP 176
GV IV+ + I+K ++A+ IK V +SL NG I +
Sbjct: 45 KKGV--IVDLDAAAQSIKKAVEAAERMAGCEIKSVIVSLSGNHIKSQNVNGEVSISEEKE 102
Query: 177 LTQEEIEKLKKSAQAIKIRD 196
+TQE+IE++ ++A+A+ I
Sbjct: 103 ITQEDIERVLEAAKAVAIPP 122
>gnl|CDD|212125 cd10814, GH38N_AMII_SpGH38_like, N-terminal catalytic domain of
SPGH38, a putative alpha-mannosidase of Streptococcus
pyogenes, and its prokaryotic homologs; glycoside
hydrolase family 38 (GH38). The subfamily is
represented by SpGH38 of Streptococcus pyogenes, which
has been assigned as a putative alpha-mannosidase, and
is encoded by ORF spy1604. SpGH38 appears to exist as an
elongated dimer and display alpha-1,3 mannosidase
activity. It is active on disaccharides and some aryl
glycosides. SpGH38 can also effectively deglycosylate
human N-glycans in vitro. A divalent metal ion, such as
a zinc ion, is required for its activity. SpGH38 is
inhibited by swainsonine. The absence of any secretion
signal peptide suggests that SpGH38 may be
intracellular.
Length = 271
Score = 29.9 bits (68), Expect = 0.78
Identities = 14/69 (20%), Positives = 26/69 (37%), Gaps = 6/69 (8%)
Query: 128 NGVTHIVNQPLTQEEI-EKLKKSAQAIKEVFLSLPCVMADNGVTHIVNQPLTQEEIEKLK 186
NG V++ +E +KL + E + S ++ NG H QP + I +
Sbjct: 178 NGNEIPVDEEEAKEFWDKKLADA-----ERYASTDHLLLMNGCDHQPVQPDLTKAIREAN 232
Query: 187 KSAQAIKIR 195
+ +
Sbjct: 233 ELYPDYEFI 241
>gnl|CDD|212670 cd10228, HSPA4_like_NDB, Nucleotide-binding domain of 105/110 kDa
heat shock proteins including HSPA4 and similar
proteins. This subgroup includes the human proteins,
HSPA4 (also known as 70-kDa heat shock protein 4, APG-2,
HS24/P52, hsp70 RY, and HSPH2; the human HSPA4 gene maps
to 5q31.1), HSPA4L (also known as 70-kDa heat shock
protein 4-like, APG-1, HSPH3, and OSP94; the human
HSPA4L gene maps to 4q28), and HSPH1 (also known as heat
shock 105kDa/110kDa protein 1, HSP105; HSP105A; HSP105B;
NY-CO-25; the human HSPH1 gene maps to 13q12.3),
Saccharomyces cerevisiae Sse1p and Sse2p, and a sea
urchin sperm receptor. It belongs to the 105/110 kDa
heat shock protein (HSP105/110) subfamily of the
HSP70-like family, and includes proteins believed to
function generally as co-chaperones of HSP70 chaperones,
acting as nucleotide exchange factors (NEFs), to remove
ADP from their HSP70 chaperone partners during the ATP
hydrolysis cycle. HSP70 chaperones assist in protein
folding and assembly, and can direct incompetent
"client" proteins towards degradation. Like HSP70
chaperones, HSP105/110s have an N-terminal
nucleotide-binding domain (NBD) and a C-terminal
substrate-binding domain (SBD). For HSP70 chaperones,
the nucleotide sits in a deep cleft formed between the
two lobes of the NBD. The two subdomains of each lobe
change conformation between ATP-bound, ADP-bound, and
nucleotide-free states. ATP binding opens up the
substrate-binding site; substrate-binding increases the
rate of ATP hydrolysis. Hsp70 chaperone activity is also
regulated by J-domain proteins.
Length = 381
Score = 29.8 bits (68), Expect = 1.1
Identities = 16/48 (33%), Positives = 23/48 (47%), Gaps = 4/48 (8%)
Query: 140 QEEIEKLKKSAQAIKEVFLSLPCVMADNGVTHIVNQPLTQEEIEKLKK 187
EKLKK A E L++ C+M D V+ + +EE E+L
Sbjct: 265 LAACEKLKKVLSANTEAPLNIECLMEDKD----VSGKIKREEFEELCA 308
>gnl|CDD|214850 smart00842, FtsA, Cell division protein FtsA. FtsA is essential
for bacterial cell division, and co-localizes to the
septal ring with FtsZ. It has been suggested that the
interaction of FtsA-FtsZ has arisen through coevolution
in different bacterial strains.
Length = 187
Score = 29.4 bits (67), Expect = 1.1
Identities = 17/79 (21%), Positives = 38/79 (48%), Gaps = 11/79 (13%)
Query: 127 DNGVTHIVNQPLTQEEIEKLKKSAQA-----IKEVFLSLPC----VMADNGVTHIVNQPL 177
GV IV+ I + + A+ I V++ + + +GV I ++ +
Sbjct: 38 RKGV--IVDIEAAARAIREAVEEAERMAGVKIDSVYVGISGRHLKSVNVSGVVAIPDKEI 95
Query: 178 TQEEIEKLKKSAQAIKIRD 196
TQE+I+++ ++A+A+ +
Sbjct: 96 TQEDIDRVLEAAKAVALPP 114
>gnl|CDD|234004 TIGR02772, Ku_bact, Ku protein, prokaryotic. Members of this
protein family are Ku proteins of non-homologous end
joining (NHEJ) DNA repair in bacteria and in at least
one member of the archaea (Archaeoglobus fulgidus). Most
members are encoded by a gene adjacent to the gene for
the DNA ligase that completes the repair. The NHEJ
system is broadly but rather sparsely distributed, being
present in about one fifth of the first 250 completed
prokarytotic genomes. A few species (e.g. Archaeoglobus
fulgidus and Bradyrhizobium japonicum) have multiple
copies that appear to represent recent paralogous family
expansion [DNA metabolism, DNA replication,
recombination, and repair].
Length = 258
Score = 29.5 bits (67), Expect = 1.1
Identities = 10/33 (30%), Positives = 16/33 (48%), Gaps = 1/33 (3%)
Query: 176 PLTQEEIEKLK-KSAQAIKIRDFVKCQVCGKVY 207
+ E+IE L +S + I+I FV +Y
Sbjct: 73 IIEDEDIESLPPESTKTIEIEAFVDADEIDPIY 105
>gnl|CDD|140299 PTZ00273, PTZ00273, oxidase reductase; Provisional.
Length = 320
Score = 29.7 bits (67), Expect = 1.2
Identities = 15/33 (45%), Positives = 19/33 (57%), Gaps = 4/33 (12%)
Query: 129 GVTHIVNQPLTQEEIEKLKKSAQAIKEVFLSLP 161
G +IV P+ QE IEK+ K A+ F SLP
Sbjct: 37 GFFYIVGHPIPQERIEKVLKMAKT----FFSLP 65
>gnl|CDD|187701 cd09277, RNase_HI_bacteria_HBD, Bacterial RNase HI containing a
hybrid binding domain (HBD) at the N-terminus.
Ribonuclease H (RNase H) enzymes are divided into two
major families, Type 1 and Type 2, based on amino acid
sequence similarities and biochemical properties. RNase
H is an endonuclease that cleaves the RNA strand of an
RNA/DNA hybrid in a sequence non-specific manner in the
presence of divalent cations. RNase H is involved in
DNA replication, repair and transcription. RNase H is
widely present in various organisms, including bacteria,
archaea and eukaryotes and most prokaryotic and
eukaryotic genomes contain multiple RNase H genes.
Despite the lack of amino acid sequence homology, Type 1
and type 2 RNase H share a main-chain fold and steric
configurations of the four acidic active-site (DEDD)
residues and have the same catalytic mechanism and
functions in cells. One of the important functions of
RNase H is to remove Okazaki fragments during DNA
replication. Prokaryotic RNase H varies greatly in
domain structures and substrate specificities.
Prokaryotes and some single-cell eukaryotes do not
require RNase H for viability. Some bacteria
distinguished from other bacterial RNase HI in the
presence of a hybrid binding domain (HBD) at the
N-terminus which is commonly present at the N-termini of
eukaryotic RNase HI. It has been reported that this
domain is required for dimerization and processivity of
RNase HI upon binding to RNA-DNA hybrids.
Length = 133
Score = 28.2 bits (64), Expect = 1.5
Identities = 16/38 (42%), Positives = 20/38 (52%), Gaps = 8/38 (21%)
Query: 174 NQPLTQEEIEKLKKSAQAIKIRDFVKCQVCGKVYKAHS 211
N+ T+E E + K + IKI FVK V KAHS
Sbjct: 88 NKEGTKEYKEFMDKIKKKIKIS-FVK--V-----KAHS 117
>gnl|CDD|217952 pfam04189, Gcd10p, Gcd10p family. eIF-3 is a multi-subunit complex
that stimulates translation initiation in vitro at
several different steps. This family corresponds to the
gamma subunit if eIF3. The Yeast protein Gcd10p has also
been shown to be part of a complex with the
methyltransferase Gcd14p that is involved in modifying
tRNA.
Length = 299
Score = 28.8 bits (65), Expect = 1.9
Identities = 15/66 (22%), Positives = 26/66 (39%), Gaps = 6/66 (9%)
Query: 127 DNGVTHIVNQPLTQEEIEKLKKSAQAIKEVFLSLPCVMADNGVTHIVN----QPLTQEEI 182
++ ++ + ++ + L + DN +IV+ Q LT EEI
Sbjct: 56 EDKELRVIGRVEVLLQLYPDSDETDSDDPETLEISESSRDN--RNIVDDGSSQKLTMEEI 113
Query: 183 EKLKKS 188
E LKK
Sbjct: 114 EALKKE 119
Score = 28.8 bits (65), Expect = 2.1
Identities = 15/36 (41%), Positives = 20/36 (55%), Gaps = 6/36 (16%)
Query: 125 MADNGVTHIVN----QPLTQEEIEKLKKSAQAIKEV 156
DN +IV+ Q LT EEIE LKK + +E+
Sbjct: 93 SRDN--RNIVDDGSSQKLTMEEIEALKKEGASGEEI 126
>gnl|CDD|215155 PLN02275, PLN02275, transferase, transferring glycosyl groups.
Length = 371
Score = 28.5 bits (64), Expect = 2.4
Identities = 12/25 (48%), Positives = 13/25 (52%), Gaps = 1/25 (4%)
Query: 36 PKELFRP-ERTVSSRKNRPKRTVSS 59
P E FRP + R NRP VSS
Sbjct: 195 PPEFFRPASLEIRLRPNRPALVVSS 219
>gnl|CDD|133425 cd05197, GH4_glycoside_hydrolases, Glycoside Hydrases Family 4.
Glycoside hydrolases cleave glycosidic bonds to release
smaller sugars from oligo- or polysaccharides. Some
bacteria simultaneously translocate and phosphorylate
disaccharides via the phosphoenolpyruvate-dependent
phosphotransferase system (PEP-PTS). After
translocation, these phospho-disaccharides may be
hydrolyzed by GH4 glycoside hydrolases. Other organisms
(such as archaea and Thermotoga maritima) lack the
PEP-PTS system, but have several enzymes normally
associated with the PEP-PTS operon. GH4 family members
include 6-phospho-beta-glucosidases,
6-phospho-alpha-glucosidases,
alpha-glucosidases/alpha-glucuronidases (only from
Thermotoga), and alpha-galactosidases. They require two
cofactors, NAD+ and a divalent metal (Mn2+, Ni2+, Mg2+),
for activity. Some also require reducing conditions. GH4
glycoside hydrolases are part of the NAD(P)-binding
Rossmann fold superfamily, which includes a wide variety
of protein families including the NAD(P)-binding domains
of alcohol dehydrogenases, tyrosine-dependent
oxidoreductases, glyceraldehyde-3-phosphate
dehydrogenases, formate/glycerate dehydrogenases,
siroheme synthases, 6-phosphogluconate dehydrogenases,
aminoacid dehydrogenases, repressor rex, and NAD-binding
potassium channel domains, among others.
Length = 425
Score = 28.6 bits (64), Expect = 2.5
Identities = 27/168 (16%), Positives = 50/168 (29%), Gaps = 30/168 (17%)
Query: 36 PKELFRPERTVSSRKNRPKRTVSSGKSCIVRKELYR-PERTVSSRKNCIVPKELY----C 90
+ + E V + + E+Y+ + S + Y
Sbjct: 260 WDKXRKLEADKEITWKTRADEVGKVEKEL--FEVYKFIKENPSVVELIKRGGRKYSEAAI 317
Query: 91 PEIEDREQDRRKPAIHLLGH------HGIEEEVFLSLPCVMADNGVTHIVNQPL------ 138
P I D ++ I+++V + +PC++ NG I PL
Sbjct: 318 PLIRALLNDNGA--RFVVNTRNNGAIANIDDDVVVEVPCLVDKNGPHPIKVGPLDRFVKG 375
Query: 139 ---TQEEIEKL------KKSAQAIKEVFLSLPCVMADNGVTHIVNQPL 177
++ E+L Q E P V +D I+ + L
Sbjct: 376 LLRQRKMRERLALEAFLTGDIQIALEALYRDPLVPSDEQAKKILEEIL 423
>gnl|CDD|133423 cd01338, MDH_choloroplast_like, Chloroplast-like malate
dehydrogenases. MDH is one of the key enzymes in the
citric acid cycle, facilitating both the conversion of
malate to oxaloacetate and replenishing levels of
oxalacetate by reductive carboxylation of pyruvate.
Members of this subfamily are bacterial MDHs, and plant
MDHs localized to the choloroplasts. MDHs are part of
the NAD(P)-binding Rossmann fold superfamily, which
includes a wide variety of protein families including
the NAD(P)-binding domains of alcohol dehydrogenases,
tyrosine-dependent oxidoreductases,
glyceraldehyde-3-phosphate dehydrogenases,
formate/glycerate dehydrogenases, siroheme synthases,
6-phosphogluconate dehydrogenases, aminoacid
dehydrogenases, repressor rex, and NAD-binding potassium
channel domains, among others.
Length = 322
Score = 28.3 bits (64), Expect = 2.7
Identities = 10/47 (21%), Positives = 17/47 (36%)
Query: 109 GHHGIEEEVFLSLPCVMADNGVTHIVNQPLTQEEIEKLKKSAQAIKE 155
G +GI E + S P G + + EK+ + + E
Sbjct: 269 GSYGIPEGLIFSFPVRSKGGGYEIVEGLEIDDFAREKIDATLAELLE 315
>gnl|CDD|235087 PRK02925, PRK02925, glucuronate isomerase; Reviewed.
Length = 466
Score = 28.6 bits (65), Expect = 2.8
Identities = 13/69 (18%), Positives = 26/69 (37%), Gaps = 21/69 (30%)
Query: 118 FLSLPCVMADNGVTHIVNQPLTQEEIEKLKKSAQAIKEVFLSLPCVMADNGVTHIVNQPL 177
F + C +D+G+ +V L++ E + + A + L
Sbjct: 227 FAAHGCRSSDHGLDTVVTAELSEAEADAIFAKA---------------------LAGGTL 265
Query: 178 TQEEIEKLK 186
T+EEI + +
Sbjct: 266 TEEEIAQFR 274
>gnl|CDD|198171 smart01103, CRS1_YhbY, Escherichia coli YhbY is associated with
pre-50S ribosomal subunits, which implies a function in
ribosome assembly. GFP fused to a single-domain CRM
protein from maize localises to the nucleolus,
suggesting that an analogous activity may have been
retained in plants. A CRM domain containing protein in
plant chloroplasts has been shown to function in group I
and II intron splicing. In vitro experiments with an
isolated maize CRM domain have shown it to have RNA
binding activity. These and other results suggest that
the CRM domain evolved in the context of ribosome
function prior to the divergence of Archaea and
Bacteria, that this function has been maintained in
extant prokaryotes, and that the domain was recruited to
serve as an RNA binding module during the evolution of
plant genomes. YhbY has a fold similar to that of the
C-terminal domain of translation initiation factor 3
(IF3C), which binds to 16S rRNA in the 30S ribosome.
Length = 84
Score = 26.7 bits (60), Expect = 2.8
Identities = 15/58 (25%), Positives = 27/58 (46%), Gaps = 10/58 (17%)
Query: 138 LTQEEIEKLKKSAQAIKEVFLSLPCVMADNGVTHIVNQPLTQEEIEKLKKSAQAIKIR 195
LT ++ L+ A +K V + NG+T V EEI++ + + IK++
Sbjct: 1 LTGKQKRYLRSLAHHLKPVVQ-----IGKNGLTEGV-----LEEIDEALEKHELIKVK 48
>gnl|CDD|239334 cd03036, ArsC_like, Arsenate Reductase (ArsC) family, unknown
subfamily; uncharacterized proteins containing a CXXC
motif with similarity to thioredoxin (TRX)-fold arsenic
reductases, ArsC. Proteins containing a redox active
CXXC motif like TRX and glutaredoxin (GRX) function as
protein disulfide oxidoreductases, altering the redox
state of target proteins via the reversible oxidation of
the active site dithiol. ArsC catalyzes the reduction of
arsenate [As(V)] to arsenite [As(III)], using reducing
equivalents derived from glutathione via GRX, through a
single catalytic cysteine.
Length = 111
Score = 27.2 bits (61), Expect = 3.1
Identities = 11/27 (40%), Positives = 19/27 (70%), Gaps = 1/27 (3%)
Query: 132 HIVNQPLTQEEIEK-LKKSAQAIKEVF 157
IV +P ++EE++K L+KS +K+ F
Sbjct: 30 DIVEEPPSKEELKKWLEKSGLPLKKFF 56
>gnl|CDD|132934 cd07023, S49_Sppa_N_C, Signal peptide peptidase A (SppA), a serine
protease, has catalytic Ser-Lys dyad. Signal peptide
peptidase A (SppA; Peptidase S49; Protease IV): SppA is
found in all three domains of life and is involved in
the cleavage of signal peptides after their removal from
the precursor proteins by signal peptidases. This
subfamily contains members with either a single domain
(sometimes referred to as 36K type), such as sohB
peptidase, protein C and archaeal signal peptide
peptidase, or an amino-terminal domain in addition to
the carboxyl-terminal protease domain that is conserved
in all the S49 family members (sometimes referred to as
67K type), similar to E. coli and Arabidopsis thaliana
SppA peptidases. Site-directed mutagenesis and sequence
analysis have shown these SppAs to be serine proteases.
The predicted active site serine for members in this
family occurs in a transmembrane domain. Mutagenesis
studies also suggest that the catalytic center comprises
a Ser-Lys dyad and not the usual Ser-His-Asp catalytic
triad found in the majority of serine proteases.
Interestingly, the single membrane spanning E. coli SppA
carries out catalysis using a Ser-Lys dyad with the
serine located in the conserved carboxy-terminal
protease domain and the lysine in the non-conserved
amino-terminal domain.
Length = 208
Score = 27.8 bits (63), Expect = 3.4
Identities = 21/79 (26%), Positives = 34/79 (43%), Gaps = 15/79 (18%)
Query: 107 LLGHHGIEEEVFLSLPCVMADNGVTHIVNQPLTQEEIEKLKKSAQAIKEVFLSLPCVMAD 166
LL GIE + S P D G ++PLT+EE L+ I + F+ + V
Sbjct: 114 LLDKLGIERDTIKSGP--GKDKG---SPDRPLTEEERAILQALVDDIYDQFVDV--VAE- 165
Query: 167 NGVTHIVNQPLTQEEIEKL 185
+ ++ E ++KL
Sbjct: 166 -------GRGMSGERLDKL 177
>gnl|CDD|220598 pfam10142, PhoPQ_related, PhoPQ-activated pathogenicity-related
protein. Members of this family of bacterial proteins
are involved in the virulence of some pathogenic
proteobacteria.
Length = 363
Score = 28.0 bits (63), Expect = 3.5
Identities = 12/55 (21%), Positives = 18/55 (32%), Gaps = 9/55 (16%)
Query: 124 VMADNGVTHIVNQPLTQEEIEKLKKSAQAIKEVFLSLPCVMADNGVTHIVNQPLT 178
++ G + P E E L A+ L + + NQPLT
Sbjct: 68 LIITGGSNRNIPGPPLDSEPEYLAGIARDTGTPVAIL---------SDVPNQPLT 113
>gnl|CDD|190184 pfam01985, CRS1_YhbY, CRS1 / YhbY (CRM) domain. Escherichia coli
YhbY is associated with pre-50S ribosomal subunits,
which implies a function in ribosome assembly. GFP fused
to a single-domain CRM protein from maize localises to
the nucleolus, suggesting that an analogous activity may
have been retained in plants. A CRM domain containing
protein in plant chloroplasts has been shown to function
in group I and II intron splicing. In vitro experiments
with an isolated maize CRM domain have shown it to have
RNA binding activity. These and other results suggest
that the CRM domain evolved in the context of ribosome
function prior to the divergence of Archaea and
Bacteria, that this function has been maintained in
extant prokaryotes, and that the domain was recruited to
serve as an RNA binding module during the evolution of
plant genomes. YhbY has a fold similar to that of the
C-terminal domain of translation initiation factor 3
(IF3C), which binds to 16S rRNA in the 30S ribosome.
Length = 84
Score = 26.3 bits (59), Expect = 4.0
Identities = 15/58 (25%), Positives = 27/58 (46%), Gaps = 10/58 (17%)
Query: 138 LTQEEIEKLKKSAQAIKEVFLSLPCVMADNGVTHIVNQPLTQEEIEKLKKSAQAIKIR 195
LT ++ L+ A +K V + NG+T V EEI++ + + IK++
Sbjct: 1 LTGKQRRYLRSLAHHLKPVVQ-----IGKNGLTEGV-----VEEIDEALEKHELIKVK 48
>gnl|CDD|130817 TIGR01756, LDH_protist, lactate dehydrogenase. This model
represents a family of protist lactate dehydrogenases
which have aparrently evolved from a recent protist
malate dehydrogenase ancestor. Lactate dehydrogenase
converts the hydroxyl at C-2 of lactate to a carbonyl in
the product, pyruvate. The preference of this enzyme for
NAD or NADP has not been determined. A critical residue
in malate dehydrogenase, arginine-91 (T. vaginalis
numbering) has been mutated to a leucine, eliminating
the positive charge which complemeted the carboxylate in
malate which is absent in lactate. Several other more
subtle changes are proposed to make the active site
smaller to accomadate the less bulky lactate molecule.
Length = 313
Score = 27.9 bits (62), Expect = 4.3
Identities = 14/46 (30%), Positives = 24/46 (52%), Gaps = 1/46 (2%)
Query: 111 HGIEEEVFLSLPCVMADNGVTHIV-NQPLTQEEIEKLKKSAQAIKE 155
+GI+ V S PC + ++G H+V N L KL ++ + + E
Sbjct: 258 YGIKPGVIFSFPCTVDEDGKVHVVENFELNPWLKTKLAQTEKDLFE 303
>gnl|CDD|200468 cd11329, AmyAc_maltase-like, Alpha amylase catalytic domain family
found in maltase. Maltase (EC 3.2.1.20) hydrolyzes the
terminal, non-reducing (1->4)-linked alpha-D-glucose
residues in maltose, releasing alpha-D-glucose. The
catalytic triad (DED) which is highly conserved in the
other maltase group is not present in this subfamily.
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 = 477
Score = 27.7 bits (62), Expect = 4.6
Identities = 15/59 (25%), Positives = 28/59 (47%), Gaps = 7/59 (11%)
Query: 141 EEIEKLKKSAQAIKEVFLSLPCVMADNGVTHIVNQPLTQEEIEKLKKSAQAIKIRDFVK 199
E +E + K K V LP AD T++ N + ++++L K+A+ I+ +
Sbjct: 83 EHVEAISKLG--AKGVIYELP---ADE--TYLNNSYGVESDLKELVKTAKQKDIKVILD 134
>gnl|CDD|233300 TIGR01174, ftsA, cell division protein FtsA. This bacterial cell
division protein interacts with FtsZ, the bacterial
homolog of tubulin. It is an ATP-binding protein and
shows structural similarities to actin and heat shock
cognate protein 70 [Cellular processes, Cell division].
Length = 371
Score = 27.6 bits (62), Expect = 4.8
Identities = 11/31 (35%), Positives = 22/31 (70%)
Query: 166 DNGVTHIVNQPLTQEEIEKLKKSAQAIKIRD 196
GV I ++ +TQE+IE++ ++A+A+ I +
Sbjct: 85 SIGVVAIKDKEVTQEDIERVLETAKAVAIPN 115
>gnl|CDD|234808 PRK00652, lpxK, tetraacyldisaccharide 4'-kinase; Reviewed.
Length = 325
Score = 27.5 bits (62), Expect = 5.0
Identities = 9/31 (29%), Positives = 14/31 (45%), Gaps = 6/31 (19%)
Query: 175 QPLTQEEIEKLKKSAQAI----KIRDFVKCQ 201
P T+ ++E L + K D VKC+
Sbjct: 267 YPFTKADLEALVSKGLTLLMTEK--DAVKCR 295
>gnl|CDD|235468 PRK05442, PRK05442, malate dehydrogenase; Provisional.
Length = 326
Score = 27.5 bits (62), Expect = 5.1
Identities = 16/52 (30%), Positives = 23/52 (44%), Gaps = 10/52 (19%)
Query: 109 GHHGIEEEVFLSLPCVMADNGVTHIVNQPLTQEEI-----EKLKKSAQAIKE 155
G +GI E + P +NG IV Q L EI EK+ + ++E
Sbjct: 271 GSYGIPEGLIFGFPVTC-ENGEYEIV-QGL---EIDDFSREKIDATLAELEE 317
>gnl|CDD|179184 PRK00961, PRK00961, H(2)-dependent methylenetetrahydromethanopterin
dehydrogenase; Provisional.
Length = 342
Score = 27.4 bits (61), Expect = 6.4
Identities = 18/68 (26%), Positives = 32/68 (47%), Gaps = 7/68 (10%)
Query: 138 LTQEEIE---KLKKSAQAIKEVFLSLPCVMADNGVTHIVNQPLTQEEIE-KLKKSAQAI- 192
+T I +L A + EV +S PC + G +++ +E +E L + + +
Sbjct: 39 MTHSTITMGAELLHLAPGVDEVVVSDPCFAEEPGFV-VIDDFDYKEVMEAHLAGNPEKVM 97
Query: 193 -KIRDFVK 199
KIR+ VK
Sbjct: 98 PKIREKVK 105
>gnl|CDD|237951 PRK15347, PRK15347, two component system sensor kinase SsrA;
Provisional.
Length = 921
Score = 27.3 bits (61), Expect = 7.0
Identities = 16/64 (25%), Positives = 28/64 (43%), Gaps = 8/64 (12%)
Query: 132 HIVNQPLTQEEIEKLKKSA-QAIKEVFLSLPCVMAD--NGVTHIVNQPLTQEEIEKLKKS 188
+ NQ + + + LK A QA L C + D N + + L+ EE+ L++
Sbjct: 856 AVENQEVLSQLLHTLKGCAGQAGLT---ELQCAVIDLENALET--GEILSLEELTDLREL 910
Query: 189 AQAI 192
A+
Sbjct: 911 IHAL 914
>gnl|CDD|234415 TIGR03955, rSAM_HydG, [FeFe] hydrogenase H-cluster radical SAM
maturase HydG. This model describes the radical SAM
protein HydG. It is part of an enzyme metallocenter
maturation system, working together with GTP-binding
protein HydF and another radical SAM enzyme, HydE, in
H-cluster maturation in [FeFe] hydrogenases [Protein
fate, Protein modification and repair].
Length = 471
Score = 27.4 bits (61), Expect = 7.3
Identities = 22/65 (33%), Positives = 29/65 (44%), Gaps = 24/65 (36%)
Query: 141 EEIEKLKKSAQAIKEVF------------LSLPCVMADNGVT---------HIVNQPLTQ 179
E+IE++ K A+ IK+ F LS CV NG HI + LTQ
Sbjct: 62 EKIEEIYKLAEQIKKKFYGNRIVMFAPLYLSNYCV---NGCVYCPYHAKNKHIARKKLTQ 118
Query: 180 EEIEK 184
EEI +
Sbjct: 119 EEIRR 123
>gnl|CDD|239835 cd04370, BAH, BAH, or Bromo Adjacent Homology domain (also called
ELM1 and BAM for Bromo Adjacent Motif). BAH domains
have first been described as domains found in the
polybromo protein and Yeast Rsc1/Rsc2 (Remodeling of
the Structure of Chromatin). They also occur in
mammalian DNA methyltransferases and the MTA1 subunits
of histone deacetylase complexes. A BAH domain is also
found in Yeast Sir3p and in the origin receptor complex
protein 1 (Orc1p), where it was found to interact with
the N-terminal lobe of the silence information
regulator 1 protein (Sir1p), confirming the initial
hypothesis that BAH plays a role in protein-protein
interactions.
Length = 123
Score = 26.2 bits (58), Expect = 7.6
Identities = 11/41 (26%), Positives = 16/41 (39%), Gaps = 1/41 (2%)
Query: 55 RTVSSGKSCIVRKELYRPERTVSSRKNCIVPKELYCPEIED 95
+ K VR YRPE T + +EL+ + D
Sbjct: 33 EDTNGSKQVKVRW-FYRPEETPKGLSPFALRRELFLSDHLD 72
>gnl|CDD|212676 cd10234, HSPA9-Ssq1-like_NBD, Nucleotide-binding domain of human
HSPA9 and similar proteins. This subfamily includes
human mitochondrial HSPA9 (also known as 70-kDa heat
shock protein 9, CSA; MOT; MOT2; GRP75; PBP74; GRP-75;
HSPA9B; MTHSP75; the gene encoding HSPA9 maps to
5q31.1), Escherichia coli DnaK, Saccharomyces cerevisiae
Stress-seventy subfamily Q protein 1/Ssq1p (also called
Ssc2p, Ssh1p, mtHSP70 homolog), and S. cerevisiae
Stress-Seventy subfamily C/Ssc1p (also called mtHSP70,
Endonuclease SceI 75 kDa subunit). It belongs to the
heat shock protein 70 (HSP70) family of chaperones that
assist in protein folding and assembly, and can direct
incompetent "client" proteins towards degradation.
Typically, HSP70s have a nucleotide-binding domain (NBD)
and a substrate-binding domain (SBD). The nucleotide
sits in a deep cleft formed between the two lobes of the
NBD. The two subdomains of each lobe change conformation
between ATP-bound, ADP-bound, and nucleotide-free
states. ATP binding opens up the substrate-binding site;
substrate-binding increases the rate of ATP hydrolysis.
Hsp70 chaperone activity is regulated by various
co-chaperones: J-domain proteins and nucleotide exchange
factors (NEFs); for Escherichia coli DnaK, these are the
DnaJ and GrpE, respectively.
Length = 376
Score = 26.8 bits (60), Expect = 7.8
Identities = 17/54 (31%), Positives = 27/54 (50%), Gaps = 3/54 (5%)
Query: 136 QPLTQEEIEKLKKSAQAIKEVFLSLPCVMAD-NGVTHIVNQPLTQEEIEKLKKS 188
Q L E EK K ++ E ++LP + AD G H+ LT+ + E+L +
Sbjct: 254 QRLK-EAAEKAKIELSSVTETEINLPFITADATGPKHLE-MTLTRAKFEELTED 305
>gnl|CDD|216498 pfam01430, HSP33, Hsp33 protein. Hsp33 is a molecular chaperone,
distinguished from all other known chaperones by its
mode of functional regulation. Its activity is redox
regulated. Hsp33 is a cytoplasmically localised protein
with highly reactive cysteines that respond quickly to
changes in the redox environment. Oxidising conditions
like H2O2 cause disulfide bonds to form in Hsp33, a
process that leads to the activation of its chaperone
function.
Length = 274
Score = 26.7 bits (60), Expect = 8.0
Identities = 10/32 (31%), Positives = 18/32 (56%), Gaps = 4/32 (12%)
Query: 177 LTQEEIEKLKKSAQAIKIRDFVKCQVCGKVYK 208
L +EE++ + + I+ V C+ CGK Y+
Sbjct: 244 LGKEELQDMIEEDGKIE----VTCEFCGKKYR 271
>gnl|CDD|237904 PRK15080, PRK15080, ethanolamine utilization protein EutJ;
Provisional.
Length = 267
Score = 26.7 bits (60), Expect = 8.9
Identities = 14/39 (35%), Positives = 19/39 (48%), Gaps = 3/39 (7%)
Query: 141 EEIEKLKKSAQAIKEVF-LSLPCV--MADNGVTHIVNQP 176
EE E+ K+ + KE+F + P V MA HI Q
Sbjct: 183 EEAEQYKRDPKHHKEIFPVVKPVVEKMASIVARHIEGQD 221
>gnl|CDD|181887 PRK09472, ftsA, cell division protein FtsA; Reviewed.
Length = 420
Score = 26.7 bits (59), Expect = 9.3
Identities = 13/48 (27%), Positives = 28/48 (58%), Gaps = 4/48 (8%)
Query: 153 IKEVFLSLP----CVMADNGVTHIVNQPLTQEEIEKLKKSAQAIKIRD 196
I V+L+L + G+ I + +TQE++E + +A+++++RD
Sbjct: 76 ISSVYLALSGKHISCQNEIGMVPISEEEVTQEDVENVVHTAKSVRVRD 123
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
0.317 0.133 0.384
Gapped
Lambda K H
0.267 0.0856 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,505,088
Number of extensions: 975293
Number of successful extensions: 1586
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1575
Number of HSP's successfully gapped: 99
Length of query: 211
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 118
Effective length of database: 6,812,680
Effective search space: 803896240
Effective search space used: 803896240
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 (21.7 bits)
S2: 57 (25.5 bits)