RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4713
(103 letters)
>gnl|CDD|218001 pfam04275, P-mevalo_kinase, Phosphomevalonate kinase.
Phosphomevalonate kinase (EC:2.7.4.2) catalyzes the
phosphorylation of 5-phosphomevalonate into
5-diphosphomevalonate, an essential step in isoprenoid
biosynthesis via the mevalonate pathway. This family
represents the animal type of the enzyme. The other is
the ERG8 type, found in plants and fungi, and some
bacteria (see pfam00288).
Length = 115
Score = 130 bits (330), Expect = 4e-41
Identities = 48/86 (55%), Positives = 67/86 (77%)
Query: 10 FSGKRKSGKDFLTDYLLERIGSQHCAIIRLSAPIKSHWAKQNGLEMDKLLGATKYKEKYR 69
FSGKRKSGKD++T+ L +R+GS C+I+R+S PIK WA+++GL++++LLG YKEKYR
Sbjct: 1 FSGKRKSGKDYVTERLQQRLGSDRCSILRISEPIKEEWARKHGLDLEELLGDGPYKEKYR 60
Query: 70 AEMITWSEAERRKDNGCFIRSAIEMA 95
+MI W E +R+KD G F R+A E A
Sbjct: 61 KDMIKWGEEKRQKDPGFFCRAACEEA 86
>gnl|CDD|130290 TIGR01223, Pmev_kin_anim, phosphomevalonate kinase, animal type.
This enzyme is part of the mevalonate pathway, one of
two alternative pathways for the biosynthesis of IPP.
In an example of nonorthologous gene displacement, two
different types of phosphomevalonate kinase are found.
One is this type, found in animals. The other is the
ERG8 type, found in plants and fungi (TIGR01219) and in
Gram-positive bacteria (TIGR01220) [Central
intermediary metabolism, Other].
Length = 182
Score = 96.7 bits (240), Expect = 9e-27
Identities = 43/87 (49%), Positives = 62/87 (71%)
Query: 7 ILLFSGKRKSGKDFLTDYLLERIGSQHCAIIRLSAPIKSHWAKQNGLEMDKLLGATKYKE 66
+LLFSGKRKSGKDF+T+ L R+G+ CA++RLS P+K +A+++GL +LL + YKE
Sbjct: 1 VLLFSGKRKSGKDFVTEALQSRLGADVCAVLRLSGPLKEQYAQEHGLNFQRLLDTSTYKE 60
Query: 67 KYRAEMITWSEAERRKDNGCFIRSAIE 93
+R +MI W E +R+ D G F R +E
Sbjct: 61 AFRKDMIRWGEEKRQADPGFFCRKIVE 87
>gnl|CDD|222885 PHA02575, 1, deoxynucleoside monophosphate kinase; Provisional.
Length = 227
Score = 31.2 bits (71), Expect = 0.057
Identities = 15/41 (36%), Positives = 25/41 (60%), Gaps = 4/41 (9%)
Query: 5 KLILLFSGKRKSGKDFLTDYLLERIGSQHCAIIRLSAPIKS 45
LI + SGK++SGKD + D+++E + +L+ PIK
Sbjct: 1 MLIAI-SGKKRSGKDTVADFIIENYNA---VKYQLADPIKE 37
>gnl|CDD|212131 cd11666, GH38N_Man2A1, N-terminal catalytic domain of Golgi
alpha-mannosidase II and similar proteins; glycoside
hydrolase family 38 (GH38). This subfamily is
represented by Golgi alpha-mannosidase II (GMII, also
known as mannosyl-oligosaccharide 1,3- 1,6-alpha
mannosidase, EC 3.2.1.114, Man2A1), a monomeric,
membrane-anchored class II alpha-mannosidase existing in
the Golgi apparatus of eukaryotes. GMII plays a key role
in the N-glycosylation pathway. It catalyzes the
hydrolysis of the terminal of both alpha-1,3-linked and
alpha-1,6-linked mannoses from the high-mannose
oligosaccharide GlcNAc(Man)5(GlcNAc)2 to yield
GlcNAc(Man)3(GlcNAc)2(GlcNAc, N-acetylglucosmine), which
is the committed step of complex N-glycan synthesis.
GMII is activated by zinc or cobalt ions and is strongly
inhibited by swainsonine. Inhibition of GMII provides a
route to block cancer-induced changes in cell surface
oligosaccharide structures. GMII has a pH optimum of
5.5-6.0, which is intermediate between those of acidic
(lysosomal alpha-mannosidase) and neutral (ER/cytosolic
alpha-mannosidase) enzymes. GMII is a retaining glycosyl
hydrolase of family GH38 that employs a two-step
mechanism involving the formation of a covalent glycosyl
enzyme complex; two carboxylic acids positioned within
the active site act in concert: one as a catalytic
nucleophile and the other as a general acid/base
catalyst.
Length = 344
Score = 27.6 bits (61), Expect = 0.98
Identities = 12/31 (38%), Positives = 18/31 (58%)
Query: 24 YLLERIGSQHCAIIRLSAPIKSHWAKQNGLE 54
YLL+R G + I R+ +K H++ Q LE
Sbjct: 135 YLLKRAGLSNMLIQRVHYSVKKHFSLQKTLE 165
>gnl|CDD|200492 cd11355, AmyAc_Sucrose_phosphorylase, Alpha amylase catalytic
domain found in sucrose phosphorylase (also called
sucrose glucosyltransferase, disaccharide
glucosyltransferase, and sucrose-phosphate alpha-D
glucosyltransferase). Sucrose phosphorylase is a
bacterial enzyme that catalyzes the phosphorolysis of
sucrose to yield glucose-1-phosphate and fructose. These
enzymes do not have the conserved calcium ion present in
other alpha amylase family enzymes. 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 = 433
Score = 26.4 bits (59), Expect = 2.8
Identities = 9/25 (36%), Positives = 14/25 (56%), Gaps = 1/25 (4%)
Query: 17 GKDFLTDYLLERIGSQHCAIIRLSA 41
GK++L L E + + +IRL A
Sbjct: 168 GKEYLESIL-EFLAANGVKLIRLDA 191
>gnl|CDD|151170 pfam10664, NdhM, Cyanobacterial and plastid NDH-1 subunit M. The
proton-pumping NADH:ubiquinone oxidoreductase catalyzes
the electron transfer from NADH to ubiquinone linked
with proton translocation across the membrane. It is
the largest, most complex and least understood of the
respiratory chain enzymes and is referred to as Complex
I. The subunit composition of the enzyme varies between
groups of organisms. Complex I originating from
mammalian mitochondria contains 45 different proteins,
whereas in bacteria, the corresponding complex NDH-1
consists of 14 different polypeptides. Homologues of
these 14 proteins are found among subunits of the
mitochondrial complex I, and therefore bacterial NDH-1
might be considered a model proton-pumping NADH
dehydrogenase with a minimal set of subunits.
Escherichia coli NDH-1 readily disintegrates into 3
sub-complexes: a water-soluble NADH dehydrogenase
fragment (NuoE, -F, and -G),the connecting fragment
(NuoB, -C, -D, and -I), and the membrane fragment
(NuoA, -H, -J, -K, -L, -M, -N). In cyanobacteria and
their descendants, the chloroplasts of green plants,
the subunit composition of NDH-1 remains obscure. The
genes for eleven subunits NdhA-NdhK, homologous to the
NuoA-NuoD and NuoH-NuoN of the E. coli complex, have
been found in the genome of Synechocystis sp. PCC 6803
which has a family of 6 ndhD genes and a family of 3
ndhF genes. Two reported multisubunit complexes, NDH-1L
and NDH-1M, represent distinct NDH-1 complexes in the
thylakoid membrane of Synechocystis 6803
-cyanobacterium. NDH-1L was shown to be essential for
photoheterotrophic cell growth, whereas expression of
NDH-1M was a prerequisite for CO2 uptake and played an
important role in growth of cells at low CO2. Here we
report the subunit composition of these two complexes.
Fifteen proteins were discovered in NDH-1L including
NdhL, a new component of the membrane fragment, and
Ssl1690 (designated as NdhO), a novel peripheral
subunit. The cyanobacterial NDH-1 complex contains
additional subunits, NdhM and NdhN, compared with the
minimal set of the bacterial enzyme and these seem to
be specific for thylakoid-located NDH-1 of
photosynthetic organisms. The three subunits of NDH-1,
NdhM, NdhN and NdhO are essential for effecting cyclic
electron flow around photosystem I, by supplying
extra-ATP for photosynthesis in both plastids and
cyanobacteria.
Length = 108
Score = 25.3 bits (56), Expect = 4.6
Identities = 12/25 (48%), Positives = 17/25 (68%), Gaps = 5/25 (20%)
Query: 16 SGKDFLTDYLLERIGS--QHCAIIR 38
+G++ L+DY L RIGS +H IR
Sbjct: 59 AGEE-LSDYNLRRIGSDLEHF--IR 80
>gnl|CDD|233903 TIGR02512, FeFe_hydrog_A, [FeFe] hydrogenase, group A. This model
describes iron-only hydrogenases of anaerobic and
microaerophilic bacteria and protozoa. This model is
narrower, and covers a longer stretch of sequence, than
pfam02906. This family represents a division among
families that belong to pfam02906, which also includes
proteins such as nuclear prelamin A recognition factor
in animals. Note that this family shows some
heterogeneity in terms of periplasmic, cytosolic, or
hydrogenosome location, NAD or NADP dependence, and
overal protein protein length.
Length = 374
Score = 25.4 bits (56), Expect = 7.3
Identities = 8/21 (38%), Positives = 15/21 (71%)
Query: 39 LSAPIKSHWAKQNGLEMDKLL 59
L A IK++WAK+ G++ + +
Sbjct: 190 LGAVIKTYWAKKMGIDPEDVY 210
>gnl|CDD|239433 cd03317, NAAAR, N-acylamino acid racemase (NAAAR), an octameric
enzyme that catalyzes the racemization of N-acylamino
acids. NAAARs act on a broad range of N-acylamino acids
rather than amino acids. Enantiopure amino acids are of
industrial interest as chiral building blocks for
antibiotics, herbicides, and drugs. NAAAR is a member of
the enolase superfamily, characterized by the presence
of an enolate anion intermediate which is generated by
abstraction of the alpha-proton of the carboxylate
substrate by an active site residue and is stabilized by
coordination to the essential Mg2+ ion.
Length = 354
Score = 25.3 bits (56), Expect = 7.4
Identities = 15/38 (39%), Positives = 19/38 (50%)
Query: 18 KDFLTDYLLERIGSQHCAIIRLSAPIKSHWAKQNGLEM 55
KD+L LL R S + APIK + + GLEM
Sbjct: 64 KDYLLPLLLGREFSHPEEVSERLAPIKGNNMAKAGLEM 101
>gnl|CDD|223272 COG0194, Gmk, Guanylate kinase [Nucleotide transport and
metabolism].
Length = 191
Score = 24.8 bits (55), Expect = 8.4
Identities = 12/30 (40%), Positives = 15/30 (50%), Gaps = 1/30 (3%)
Query: 1 MTQPKLILLFSGKRKSGKDFLTDYLLERIG 30
M++ LI+L SG GK L LLE
Sbjct: 1 MSKGLLIVL-SGPSGVGKSTLVKALLEDDK 29
>gnl|CDD|223962 COG1031, COG1031, Uncharacterized Fe-S oxidoreductase [Energy
production and conversion].
Length = 560
Score = 25.0 bits (55), Expect = 9.7
Identities = 6/36 (16%), Positives = 12/36 (33%)
Query: 28 RIGSQHCAIIRLSAPIKSHWAKQNGLEMDKLLGATK 63
R+G Q + + N ++KL +
Sbjct: 236 RLGRQADIFSYGADDNGGEVPRPNPEALEKLFRGIR 271
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
0.321 0.134 0.398
Gapped
Lambda K H
0.267 0.0734 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,221,991
Number of extensions: 433649
Number of successful extensions: 370
Number of sequences better than 10.0: 1
Number of HSP's gapped: 370
Number of HSP's successfully gapped: 15
Length of query: 103
Length of database: 10,937,602
Length adjustment: 69
Effective length of query: 34
Effective length of database: 7,877,176
Effective search space: 267823984
Effective search space used: 267823984
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 53 (24.2 bits)