RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17092
(183 letters)
>gnl|CDD|200106 TIGR01456, CECR5, HAD-superfamily class IIA hydrolase, TIGR01456,
CECR5. This hypothetical equivalog is a member of the
Class IIA subfamily of the haloacid dehalogenase
superfamily of aspartate-nucleophile hydrolases. The
sequences modelled by this equivalog are all eukaryotes.
One sequence (GP|13344995) is called "Cat Eye Syndrome
critical region protein 5" (CECR5). This gene has been
cloned from a pericentromere region of human chromosome
22 believed to be the location of the gene or genes
responsible for Cat Eye Syndrome. This is one of a
number of candidate genes. The Schizosaccharomyces pombe
sequence (EGAD|138276) is annotated as "phosphatidyl
synthase," however this is due entirely to a C-terminal
region of the protein (outside the region of similarity
of This model) which is highly homologous to a family of
CDP-alcohol phosphatidyltransferases. (Thus, the
annotation of GP|4226073 from C. elegans as similar to
phosphatidyl synthase, is a mistake as this gene does
not contain the C-terminal portion). The physical
connection of the phosphatidyl synthase and the
HAD-superfamily hydrolase domain in S. pombe may,
however, be an important clue to the substrate for the
hydrolases in this equivalog.
Length = 321
Score = 124 bits (313), Expect = 6e-35
Identities = 46/140 (32%), Positives = 68/140 (48%), Gaps = 5/140 (3%)
Query: 7 FGLIFDIDGVLVRGKQVLPGVQDTFMNKLTNSGGRFVVPTVFVTNAGNSLAADKAKQLTE 66
FG FDIDGVL RGK+ + G D +L + G+ +P +F+TN G +A++++
Sbjct: 1 FGFAFDIDGVLFRGKKPIAGASDAL-RRLNRNQGQLKIPYIFLTNGGGFSERARAEEISS 59
Query: 67 WLGVEVEEDQVVMSHTPIKMLHKYHTKHTLISGQGPMEEIAKRLGFNKVVTVDSIRNAHP 126
LGV+V QV+ SH+P K L + K L G G + +A+ GF VV D I
Sbjct: 60 LLGVDVSPLQVIQSHSPYKSLVNKYEKRILAVGTGSVRGVAEGYGFQNVVHQDEIVRYFR 119
Query: 127 LLD----CVDHRRRVSLFPR 142
+D D +
Sbjct: 120 DIDPFSGMSDEQVMEYSRDI 139
>gnl|CDD|205524 pfam13344, Hydrolase_6, Haloacid dehalogenase-like hydrolase. This
family is part of the HAD superfamily.
Length = 101
Score = 85.6 bits (213), Expect = 3e-22
Identities = 37/106 (34%), Positives = 54/106 (50%), Gaps = 8/106 (7%)
Query: 9 LIFDIDGVLVRGKQVLPGVQDTFMNKLTNSGGRFVVPTVFVTNAGNSLAADKAKQLTEWL 68
+FD+DGVL RG + +PG + N L +G P VFVTN + AK+L + L
Sbjct: 1 FLFDVDGVLWRGGEPIPGAAEAL-NALRAAG----KPVVFVTNNSSRSREQYAKKLRK-L 54
Query: 69 GVEVEEDQVVMSHTPIK-MLHK-YHTKHTLISGQGPMEEIAKRLGF 112
G +V+ED+V+ S T L + K L+ G + E + GF
Sbjct: 55 GFDVDEDEVITSATAAADYLKERKFGKKVLVIGSEGLREELEEAGF 100
>gnl|CDD|233422 TIGR01460, HAD-SF-IIA, Haloacid Dehalogenase Superfamily Class
(subfamily) IIA. This model represents one structural
subclass of the Haloacid Dehalogenase (HAD) superfamily
of aspartate-nucleophile hydrolases. The superfamily is
defined by the presence of three short catalytic motifs.
The classes are defined based on the location and the
observed or predicted fold of a so-called "capping
domain", or the absence of such a domain. Class I
consists of sequences in which the capping domain is
found in between the first and second catalytic motifs.
Class II consists of sequences in which the capping
domain is found between the second and third motifs.
Class III sequences have no capping domain in iether of
these positions. The Class IIA capping domain is
predicted by PSI-PRED to consist of a mixed alpha-beta
fold with the basic pattern:
Helix-Helix-Helix-Sheet-Helix-Loop-Sheet-Helix-Sheet-
Helix. Presently, this subfamily encompasses a single
equivalog model (TIGR01452) for the eukaryotic
phosphoglycolate phosphatase, as well as four
hypothetical equivalogs covering closely related
sequences (TIGR01456 and TIGR01458 in eukaryotes,
TIGR01457 in gram positive bacteria and TIGR01459 in
gram negative bacteria). The Escherishia coli NagD gene
and the Bacillus subtilus AraL gene are members of this
subfamily but are not members of the any of the
presently defined equivalogs within it. NagD is part of
the NAG operon responsible for N-acetylglucosamine
metabolism. The function of this gene is unknown. Genes
from several organisms have been annotated as NagD, or
NagD-like. However, without data on the presence of
other members of this pathway, (such as in the case of
Yersinia pestis) these assignments should not be given
great weight. The AraL gene is similar: it is part of
the L-arabinose operon, but the function is unknown. A
gene from Halobacterium has been annotated as AraL, but
no other Ara operon genes have been annotated. Many of
the genes in this subfamily have been annotated as
"pNPPase" "4-nitrophenyl phosphatase" or "NPPase". These
all refer to the same activity versus a common lab test
compound used to determine phosphatase activity. There
is no evidence that this activity is physiologically
relevant [Unknown function, Enzymes of unknown
specificity].
Length = 236
Score = 77.0 bits (190), Expect = 1e-17
Identities = 37/112 (33%), Positives = 57/112 (50%), Gaps = 7/112 (6%)
Query: 10 IFDIDGVLVRGKQVLPGVQDTFMNKLTNSGGRFVVPTVFVTNAGNSLAADKAKQLTEWLG 69
+FDIDGVL G + +PG + N+L G P VF+TN + D A++L+ LG
Sbjct: 2 LFDIDGVLWLGHKPIPGAAEAL-NRLRAKG----KPVVFLTNNSSRSEEDYAEKLSSLLG 56
Query: 70 VEVEEDQVVMSHTPIK-MLHKYHT-KHTLISGQGPMEEIAKRLGFNKVVTVD 119
V+V DQ++ S + K +L + + + G G + E + LGF D
Sbjct: 57 VDVSPDQIITSGSVTKDLLRQRFEGEKVYVIGVGELRESLEGLGFRNDFFDD 108
>gnl|CDD|223720 COG0647, NagD, Predicted sugar phosphatases of the HAD superfamily
[Carbohydrate transport and metabolism].
Length = 269
Score = 73.8 bits (182), Expect = 3e-16
Identities = 36/126 (28%), Positives = 55/126 (43%), Gaps = 12/126 (9%)
Query: 8 GLIFDIDGVLVRGKQVLPGVQDTFMNKLTNSGGRFVVPTVFVTNAGNSLAADKAKQLTEW 67
G +FD+DGVL RG + +PG + + +L +G + F+TN A +L+
Sbjct: 10 GFLFDLDGVLYRGNEAIPGAAE-ALKRLKAAGKPVI----FLTNNSTRSREVVAARLSSL 64
Query: 68 LGVEVEEDQVVMSHTP-IKMLHKYHT-KHTLISGQGPMEEIAKRLGFNKVVTVDSIRNAH 125
GV+V D +V S L K K + G+ ++E + GF VD A
Sbjct: 65 GGVDVTPDDIVTSGDATADYLAKQKPGKKVYVIGEEGLKEELEGAGF---ELVDEEEPAR 121
Query: 126 PLLDCV 131
D V
Sbjct: 122 V--DAV 125
>gnl|CDD|178251 PLN02645, PLN02645, phosphoglycolate phosphatase.
Length = 311
Score = 43.2 bits (102), Expect = 3e-05
Identities = 25/71 (35%), Positives = 40/71 (56%), Gaps = 6/71 (8%)
Query: 10 IFDIDGVLVRGKQVLPGVQDTFMNKLTNSGGRFVVPTVFVTNAGNSLAADKAKQLTEWLG 69
IFD DGV+ +G +++ GV +T ++ L + G + VFVTN A K+ E LG
Sbjct: 32 IFDCDGVIWKGDKLIEGVPET-LDMLRSMGKKL----VFVTNNSTKSRAQYGKKF-ESLG 85
Query: 70 VEVEEDQVVMS 80
+ V E+++ S
Sbjct: 86 LNVTEEEIFSS 96
>gnl|CDD|119389 cd01427, HAD_like, Haloacid dehalogenase-like hydrolases. The
haloacid dehalogenase-like (HAD) superfamily includes
L-2-haloacid dehalogenase, epoxide hydrolase,
phosphoserine phosphatase, phosphomannomutase,
phosphoglycolate phosphatase, P-type ATPase, and many
others, all of which use a nucleophilic aspartate in
their phosphoryl transfer reaction. All members possess
a highly conserved alpha/beta core domain, and many also
possess a small cap domain, the fold and function of
which is variable. Members of this superfamily are
sometimes referred to as belonging to the DDDD
superfamily of phosphohydrolases.
Length = 139
Score = 38.5 bits (90), Expect = 4e-04
Identities = 21/125 (16%), Positives = 43/125 (34%), Gaps = 24/125 (19%)
Query: 9 LIFDIDGVLVRGK---------QVLPGVQDTFMNKLTNSGGRFVVPTVFVTNAGNSLAAD 59
++FD+DG L+ + ++ PGV++ + +L G + TN +
Sbjct: 2 VLFDLDGTLLDSEPGIAEIEELELYPGVKEA-LKELKEKG----IKLALATNKSRREVLE 56
Query: 60 KAKQLTEWLGVEVEEDQVVMS-HTPIKMLHKYHTKHTLIS-----GQGPMEEIAKRLGFN 113
++ LG++ D V+ S I + + K LG +
Sbjct: 57 LLEE----LGLDDYFDPVITSNGAAIYYPKEGLFLGGGPFDIGKPNPDKLLAALKLLGVD 112
Query: 114 KVVTV 118
+
Sbjct: 113 PEEVL 117
>gnl|CDD|233420 TIGR01452, PGP_euk, phosphoglycolate/pyridoxal phosphate
phosphatase family. PGP is an essential enzyme in the
glycolate salvage pathway in higher organisms
(photorespiration in plants). Phosphoglycolate results
from the oxidase activity of RubisCO in the Calvin cycle
when concentrations of carbon dioxide are low relative
to oxygen. In mammals, PGP is found in many tissues,
notably in red blood cells where P-glycolate is and
important activator of the hydrolysis of
2,3-bisphosphoglycerate, a major modifier of the oxygen
affinity of hemoglobin. Pyridoxal phosphate (PLP,
Vitamin B6) phosphatase is involved in the degradation
of PLP in mammals and is widely distributed in human
tissues including erythrocyes. The enzymes described
here are members of the Haloacid dehalogenase
superfamily of hydrolase enzymes (pfam00702). Unlike the
bacterial PGP equivalog (TIGR01449), which is a member
of class (subfamily) I, these enzymes are members of
class (subfamily) II. These two families have almost
certainly arisen from convergent evolution (although
these two ancestors may themselves have diverged from a
more distant HAD superfamily progenitor). The primary
seed sequence for this model comes from Chlamydomonas
reinhardtii, a photosynthetic alga. The enzyme has been
purified and characterized and these data are fully
consistent with the assignment of function as a PGPase
involved in photorespiration. The second seed, from Homo
sapiens chromosome 22 has been characterized as a
pyridoxal phosphatase. Biochemical characterization of
partially purified PGP's from various tissues including
red blood cells have been performed while one gene for
PGP has been localized to chromosome 16p13.3. The
sequence used here maps to chromosome 22. There is
indeed a related gene on chromosome 16 (and it is
expressed, since EST's are found) which shows 46%
identity and 59% positives by BLAST2 (E=1e-66). The
chromosome 16 gene is not in evidence in nraa but
translated from the genomic sequence would score 372.4
(E=7.9e-113) versus This model, well above trusted. The
third seed, from C. elegans, is only supported by
sequence similarity. This model is limited to eukaryotic
species including S. pombe and S. cerevisiae, although
several archaea score between the trusted and noise
cutoffs. This model is closely related to a family of
bacterial sequences including the E. coli NagD and B.
subtilus AraL genes which are characterized by the
ability to hydrolyze para-nitrophenylphosphate (pNPPases
or NPPases). The chlamydomonas PGPase d.
Length = 279
Score = 35.2 bits (81), Expect = 0.010
Identities = 28/103 (27%), Positives = 47/103 (45%), Gaps = 10/103 (9%)
Query: 8 GLIFDIDGVLVRGKQVLPGVQDTFMNKLTNSGGRFVVPTVFVTNAGNSLAADKAKQLTEW 67
G IFD DGVL G++V+PG + +++L +G +FVTN A+ A +
Sbjct: 4 GFIFDCDGVLWLGERVVPGAPEL-LDRLARAGKA----ALFVTNNSTKSRAEYALKFAR- 57
Query: 68 LGVEVEEDQVVMS-HTPIKMLHK---YHTKHTLISGQGPMEEI 106
LG +Q+ S ++L + +I +G E+
Sbjct: 58 LGFNGLAEQLFSSALCAARLLRQPPDAPKAVYVIGEEGLRAEL 100
>gnl|CDD|182466 PRK10444, PRK10444, UMP phosphatase; Provisional.
Length = 248
Score = 32.1 bits (73), Expect = 0.11
Identities = 20/67 (29%), Positives = 34/67 (50%), Gaps = 6/67 (8%)
Query: 9 LIFDIDGVLVRGKQVLPGVQDTFMNKLTNSGGRFVVPTVFVTNAGNSLAADKAKQLTEWL 68
+I DIDGVL+ +PG F++++ + G +P V +TN + D A +
Sbjct: 4 VICDIDGVLMHDNVAVPG-AAEFLHRILDKG----LPLVLLTNYPSQTGQDLANRFAT-A 57
Query: 69 GVEVEED 75
GV+V +
Sbjct: 58 GVDVPDS 64
>gnl|CDD|213673 TIGR02009, PGMB-YQAB-SF, beta-phosphoglucomutase family hydrolase.
This subfamily model groups together three clades: the
characterized beta-phosphoglucomutases (including those
from E.coli, B.subtilus and L.lactis, TIGR01990), a
clade of putative bPGM's from mycobacteria and a clade
including the uncharacterized E.coli and H.influenzae
yqaB genes which may prove to be beta-mutases of a
related 1-phosphosugar. All of these are members of the
larger Haloacid dehalogenase (HAD) subfamily IA and
include the "variant 3" glu-asp version of the third
conserved HAD domain (TIGR01509).
Length = 185
Score = 30.0 bits (68), Expect = 0.43
Identities = 29/141 (20%), Positives = 50/141 (35%), Gaps = 22/141 (15%)
Query: 8 GLIFDIDGVLVRG--------KQVLPGVQDTF---MNKLTNSGGRFVVPTVFVTNAGNSL 56
+IFD+DGV+ K + +F N+ R + + G+ L
Sbjct: 3 AVIFDMDGVITDTAPLHAQAWKHIAAKYGISFDKQYNESLKGLSREDILRAILKLRGDGL 62
Query: 57 AADKAKQLTEW---LGVEVEEDQVVMSHTPIKMLHKYHTKHTLISGQGPMEEIAKRL--- 110
+ ++ QL E L E+ V I+ L K + G G + A R+
Sbjct: 63 SLEEIHQLAERKNELYRELLRLTGVAVLPGIRNLLKRLKAKGIAVGLGSSSKNAPRILAK 122
Query: 111 -----GFNKVVTVDSIRNAHP 126
F+ +V ++N P
Sbjct: 123 LGLRDYFDAIVDASEVKNGKP 143
>gnl|CDD|130524 TIGR01457, HAD-SF-IIA-hyp2, HAD-superfamily subfamily IIA
hydrolase, TIGR01457. This hypothetical equivalog is a
member of the Class IIA subfamily of the haloacid
dehalogenase superfamily of aspartate-nucleophile
hydrolases. The sequences modelled by this equivalog
are all gram positive (low-GC) bacteria. Sequences
found in This model are annotated variously as related
to NagD or 4-nitrophenyl phosphatase, and this
hypothetical equivalog, of all of those within the
Class IIA subfamily, is most closely related to the E.
coli NagD enzyme and the PGP_euk equivalog (TIGR01452).
However, there is presently no evidence that this
hypothetical equivalog has the same function of either
those [Unknown function, Enzymes of unknown
specificity].
Length = 249
Score = 30.2 bits (68), Expect = 0.52
Identities = 14/44 (31%), Positives = 21/44 (47%), Gaps = 5/44 (11%)
Query: 8 GLIFDIDGVLVRGKQVLPGVQDTFMNKLTNSGGRFVVPTVFVTN 51
G + D+DG + G + + F+ L G VP +FVTN
Sbjct: 3 GYLIDLDGTMYNGTEKIEEAC-EFVRTLKKRG----VPYLFVTN 41
>gnl|CDD|115061 pfam06379, RhaT, L-rhamnose-proton symport protein (RhaT). This
family consists of several bacterial L-rhamnose-proton
symport protein (RhaT) sequences.
Length = 344
Score = 29.9 bits (67), Expect = 0.71
Identities = 28/113 (24%), Positives = 46/113 (40%), Gaps = 3/113 (2%)
Query: 3 LSPSFGLIFDIDGVLVRGKQVLPGVQDTFMNKLTNSGGRFVVPTVFVTNAGNSLAADKAK 62
L S G+ I L+ G + P + F + GGR + VFV G ++ + +A
Sbjct: 97 LGMSMGIGIAIGITLIIGTLMTPIINGNFDVLIGTEGGRMTLLGVFVALIGVAIVS-RAG 155
Query: 63 QLTEW-LGVEVEEDQVVMSHTPIKMLHKYHTKHTL-ISGQGPMEEIAKRLGFN 113
L E +G++ EE + M + + + PM E A LG +
Sbjct: 156 LLKERAMGIKAEEFNLKKGLILAVMCGIFSAGMSFAMDAAKPMHEAAAALGID 208
>gnl|CDD|130526 TIGR01459, HAD-SF-IIA-hyp4, HAD-superfamily class IIA hydrolase,
TIGR01459. This hypothetical equivalog is a member of
the Class IIA subfamily of the haloacid dehalogenase
superfamily of aspartate-nucleophile hydrolases. The
sequences modelled by this equivalog are all gram
negative and primarily alpha proteobacteria. Only one
sequence hase been annotated as other than
"hypothetical." That one, from Brucella, is annotated
as related to NagD, but only by sequence similarity and
should be treated with some skepticism. (See comments
for Class IIA subfamily model).
Length = 242
Score = 29.9 bits (67), Expect = 0.73
Identities = 15/60 (25%), Positives = 24/60 (40%), Gaps = 6/60 (10%)
Query: 8 GLIFDIDGVLVRGKQVLPGVQDTFMNKLTNSGGRFVVPTVFVTNAGNSLAADKAKQLTEW 67
+ D+ GV++ G PG +NK+ G P FV+N+ + K L
Sbjct: 10 VFLLDLWGVIIDGNHTYPGAVQN-LNKIIAQGK----PVYFVSNSPRN-IFSLHKTLKSL 63
>gnl|CDD|166653 PLN03012, PLN03012, Camelliol C synthase.
Length = 759
Score = 30.0 bits (67), Expect = 0.76
Identities = 15/58 (25%), Positives = 23/58 (39%)
Query: 82 TPIKMLHKYHTKHTLISGQGPMEEIAKRLGFNKVVTVDSIRNAHPLLDCVDHRRRVSL 139
P+ K L +G P +E N ++ + RN PL ++R RV L
Sbjct: 701 IPLHRAAKLIINSQLENGDFPQQEATGAFLKNCLLHYAAYRNIFPLWALAEYRARVPL 758
>gnl|CDD|224969 COG2058, RPP1A, Ribosomal protein L12E/L44/L45/RPP1/RPP2
[Translation, ribosomal structure and biogenesis].
Length = 109
Score = 28.1 bits (63), Expect = 1.1
Identities = 11/25 (44%), Positives = 13/25 (52%)
Query: 50 TNAGNSLAADKAKQLTEWLGVEVEE 74
AG + D K + E GVEVEE
Sbjct: 11 HLAGKEITEDNLKSVLEAAGVEVEE 35
>gnl|CDD|216069 pfam00702, Hydrolase, haloacid dehalogenase-like hydrolase. This
family is structurally different from the alpha/beta
hydrolase family (pfam00561). This family includes
L-2-haloacid dehalogenase, epoxide hydrolases and
phosphatases. The structure of the family consists of
two domains. One is an inserted four helix bundle,
which is the least well conserved region of the
alignment, between residues 16 and 96 of Pseudomonas
sp. (S)-2-haloacid dehalogenase 1. The rest of the fold
is composed of the core alpha/beta domain. Those
members with the characteristic DxD triad at the
N-terminus are probably phosphatidylglycerolphosphate
(PGP) phosphatases involved in cardiolipin biosynthesis
in the mitochondria.
Length = 187
Score = 28.8 bits (64), Expect = 1.2
Identities = 8/20 (40%), Positives = 14/20 (70%)
Query: 9 LIFDIDGVLVRGKQVLPGVQ 28
++FD+DG L G+ V+P +
Sbjct: 4 VVFDLDGTLTDGEPVVPEAE 23
>gnl|CDD|188973 cd09574, SAM_STIM2, SAM domain of STIM2 subfamily proteins. SAM
(sterile alpha motif) domain of STIM2 (Stromal
interaction molecule) subfamily proteins is a putative
protein-protein interaction domain. STIM1 and STIM2
human proteins are type I transmembrane proteins. The
N-terminal part of them includes "hidden" EF-hand and
SAM domains. This region is responsible for sensing
changes in store-operated and basal cytoplasmic Ca2+
levels and initiates oligomerization. "Hidden" EF hand
and SAM domains have a stable intramolecular
association, and the SAM domain is a component that
regulates stability within STIM proteins.
Destabilization of the EF-SAM association during Ca2+
depletion leads to partial unfolding and aggregation
(homooligomerization), thus activating the
store-operated Ca2+ entry. Immunoprecipitation analysis
indicates that STIM1 and STIM2 can form co-precipitable
oligomeric associations in vivo. It was suggested that
STIM2 protein is an inhibitor of store operated channels
in plasma membrane.
Length = 74
Score = 27.3 bits (60), Expect = 1.3
Identities = 13/37 (35%), Positives = 20/37 (54%), Gaps = 2/37 (5%)
Query: 132 DHRRRVSLFPRYCSRAQSLLSSELKITDRSLDHKAKI 168
D+ + + PR S + S+LKI DRS H+ K+
Sbjct: 29 DNNVKGTTLPRIAVNEPSFMISQLKILDRS--HRQKL 63
>gnl|CDD|232824 TIGR00099, Cof-subfamily, Cof subfamily of IIB subfamily of
haloacid dehalogenase superfamily. This subfamily of
sequences falls within the Class-IIB subfamily
(TIGR01484) of the Haloacid Dehalogenase superfamily of
aspartate-nucleophile hydrolases. The use of the name
"Cof" as an identifier here is arbitrary and refers to
the E. coli Cof protein. This subfamily is notable for
the large number of recent paralogs in many species.
Listeria, for instance, has 12, Clostridium,
Lactococcus and Streptococcus pneumoniae have 8 each,
Enterococcus and Salmonella have 7 each, and Bacillus
subtilus, Mycoplasma, Staphylococcus and E. coli have 6
each. This high degree of gene duplication is limited
to the gamma proteobacteria and low-GC gram positive
lineages. The profusion of genes in this subfamily is
not coupled with a high degree of divergence, so it is
impossible to determine an accurate phylogeny at the
equivalog level. Considering the relationship of this
subfamily to the other known members of the HAD-IIB
subfamily (TIGR01484), sucrose and trehalose
phosphatases and phosphomannomutase, it seems a
reasonable hypothesis that these enzymes act on
phosphorylated sugars. Possibly the diversification of
genes in this subfamily represents the diverse sugars
and polysaccharides that various bacteria find in their
biological niches. The members of this subfamily are
restricted almost exclusively to bacteria (one
sequences from S. pombe scores above trusted, while
another is between trusted and noise). It is notable
that no archaea are found in this group, the closest
relations to the archaea found here being two
Deinococcus sequences [Unknown function, Enzymes of
unknown specificity].
Length = 256
Score = 28.4 bits (64), Expect = 1.9
Identities = 10/39 (25%), Positives = 18/39 (46%), Gaps = 2/39 (5%)
Query: 9 LIFDIDGVLVR-GKQVLPGVQDTFMNKLTNSGGRFVVPT 46
+ D+DG L+ + P ++ KL G + V+ T
Sbjct: 2 IFIDLDGTLLNDDHTISPSTKEALA-KLREKGIKVVLAT 39
>gnl|CDD|240039 cd04683, Nudix_Hydrolase_24, Members of the Nudix hydrolase
superfamily catalyze the hydrolysis of NUcleoside
DIphosphates linked to other moieties, X. Enzymes
belonging to this superfamily require a divalent
cation, such as Mg2+ or Mn2+, for their activity and
contain a highly conserved 23-residue nudix motif
(GX5EX7REUXEEXGU, where U = I, L or V), which functions
as a metal binding and catalytic site. Substrates of
nudix hydrolases include intact and oxidatively damaged
nucleoside triphosphates, dinucleoside polyphosphates,
nucleotide-sugars and dinucleotide enzymes. These
substrates are metabolites or cell signaling molecules
that require regulation during different stages of the
cell cycle or during periods of stress. In general, the
role of the nudix hydrolase is to sanitize the
nucleotide pools and to maintain cell viability,
thereby serving as surveillance & "house-cleaning"
enzymes. Substrate specificity is used to define
families within the superfamily. Differences in
substrate specificity are determined by the N-terminal
extension or by residues in variable loop regions.
Mechanistically, substrate hydrolysis occurs by a
nucleophilic substitution reaction, with variation in
the numbers and roles of divalent cations required.
Length = 120
Score = 27.7 bits (62), Expect = 2.1
Identities = 14/74 (18%), Positives = 33/74 (44%), Gaps = 11/74 (14%)
Query: 12 DIDGVLVRGKQVLPGVQDTFMNKLTNSG---GRFVVPTVFVTNAGNSLAADKAKQLTEWL 68
+ +L R +VL + + N+G G++ +P + G ++ E +
Sbjct: 2 AVYVLLRRDDEVL-------LQRRANTGYMDGQWALPAGHL-EKGEDAVTAAVREAREEI 53
Query: 69 GVEVEEDQVVMSHT 82
GV ++ + + ++HT
Sbjct: 54 GVTLDPEDLRLAHT 67
>gnl|CDD|219777 pfam08282, Hydrolase_3, haloacid dehalogenase-like hydrolase.
This family contains haloacid dehalogenase-like
hydrolase enzymes.
Length = 254
Score = 28.0 bits (63), Expect = 2.4
Identities = 15/64 (23%), Positives = 27/64 (42%), Gaps = 10/64 (15%)
Query: 9 LIFDIDGVLVR-GKQVLPGVQDTFMNKLTNSGGRFVVPTVFVTNAGNSLAADKAKQLTEW 67
+ D+DG L+ K++ ++ KL G + V+ T G A + E
Sbjct: 1 IASDLDGTLLNSDKKISERTKEAIK-KLQEKGIKVVIAT------GRPYRG--ALPVLEE 51
Query: 68 LGVE 71
LG++
Sbjct: 52 LGLD 55
>gnl|CDD|184940 PRK14977, PRK14977, bifunctional DNA-directed RNA polymerase A'/A''
subunit; Provisional.
Length = 1321
Score = 28.5 bits (63), Expect = 2.5
Identities = 25/128 (19%), Positives = 48/128 (37%), Gaps = 8/128 (6%)
Query: 27 VQDTFMNKLTNSGGRFVVPTVFVTNAGNSLAADKAKQ--LTEWLGVEVEEDQVVMSHTPI 84
V F+NK+ + ++ F G+ + D+AKQ + G++ E ++
Sbjct: 644 VAIEFLNKILIIAKKEILHYGFSNGPGDLIIPDEAKQEIEDDIQGMKDEVSDLIDQRKIT 703
Query: 85 KMLHKYHTKHTLISGQGPMEEIAKRLGFNKVVTVDSIRN--AHPLLDCVDHRRRVSLFPR 142
+ + Y K L+ G E L + V +D R+ DC+D + +
Sbjct: 704 RKITIYKGKEELLRGMKEEE----ALEADIVNELDKARDKAGSSANDCIDADNAGKIMAK 759
Query: 143 YCSRAQSL 150
+R
Sbjct: 760 TGARGSMA 767
>gnl|CDD|188903 cd09504, SAM_STIM-1,2-like, SAM domain of STIM-1,2-like proteins.
SAM (sterile alpha motif) domain of STIM-1,2-like
(Stromal interaction molecule) proteins is a putative
protein-protein interaction domain. STIM1 and STIM2
human proteins are type I transmembrane proteins. The
N-terminal part of them includes "hidden" EF-hand and
SAM domains. This region is responsible for sensing
changes in store-operated and basal cytoplasmic Ca2+
levels and initiates oligomerization. "Hidden" EF hand
and SAM domains have a stable intramolecular
association, and the SAM domain is a component that
regulates stability within STIM proteins.
Destabilization of the EF-SAM association during Ca2+
depletion leads to partial unfolding and aggregation
(homooligomerization), thus activating the
store-operated Ca2+ entry. Immunoprecipitation analysis
indicates that STIM1 and STIM2 can form co-precipitable
oligomeric associations in vivo. It was suggested that
STIM1 and STIM2 are involved in opposite regulation of
store operated channels in plasma membrane.
Length = 74
Score = 25.8 bits (57), Expect = 5.5
Identities = 11/31 (35%), Positives = 14/31 (45%), Gaps = 2/31 (6%)
Query: 138 SLFPRYCSRAQSLLSSELKITDRSLDHKAKI 168
S PR S L+S L I D H+ K+
Sbjct: 35 SALPRLAVNNPSFLTSVLGIKDPI--HRQKL 63
>gnl|CDD|221799 pfam12833, HTH_18, Helix-turn-helix domain.
Length = 80
Score = 25.6 bits (57), Expect = 6.3
Identities = 9/36 (25%), Positives = 16/36 (44%), Gaps = 3/36 (8%)
Query: 81 HTPIKMLHKY---HTKHTLISGQGPMEEIAKRLGFN 113
+P + L + + L+ + EIA LGF+
Sbjct: 22 LSPKEYLRELRLERARRLLLETGLSVTEIALALGFS 57
>gnl|CDD|140329 PTZ00308, PTZ00308, ethanolamine-phosphate cytidylyltransferase;
Provisional.
Length = 353
Score = 26.7 bits (59), Expect = 7.2
Identities = 23/66 (34%), Positives = 34/66 (51%), Gaps = 7/66 (10%)
Query: 31 FMNKLT-NSGGRFV-VPTVF-VTNAGNSLAADKAKQLTEWLGVEVEEDQVVM----SHTP 83
F N + G R V V F + + G+ KA++L ++L V V EDQVV S+ P
Sbjct: 182 FSNNRSPKPGDRIVYVDGSFDLFHIGHIRVLQKARELGDYLIVGVHEDQVVNEQKGSNYP 241
Query: 84 IKMLHK 89
I L++
Sbjct: 242 IMNLNE 247
>gnl|CDD|238948 cd01990, Alpha_ANH_like_I, This is a subfamily of Adenine
nucleotide alpha hydrolases superfamily. Adenine
nucleotide alpha hydrolases superfamily includes N type
ATP PPases and ATP sulphurylases. It forms a
apha/beta/apha fold which binds to Adenosine group.
This subfamily of proteins probably binds ATP. This
domain is about 200 amino acids long with a strongly
conserved motif SGGKD at the N terminus.
Length = 202
Score = 26.4 bits (59), Expect = 7.9
Identities = 15/64 (23%), Positives = 27/64 (42%), Gaps = 11/64 (17%)
Query: 59 DKAKQLTEWLGVEVEEDQVVMSHTPIKMLHK------YHTKHTLISGQGPMEEIAKRLGF 112
++AK+L + +G+ E + K Y K L ++EIA+ LG
Sbjct: 42 EEAKRLAKEIGIRHEV--IETDELDDPEFAKNPPDRCYLCKKALYEA---LKEIAEELGL 96
Query: 113 NKVV 116
+ V+
Sbjct: 97 DVVL 100
>gnl|CDD|225237 COG2362, DppA, D-aminopeptidase [Amino acid transport and
metabolism].
Length = 274
Score = 26.6 bits (59), Expect = 7.9
Identities = 11/30 (36%), Positives = 19/30 (63%), Gaps = 2/30 (6%)
Query: 40 GRFVVPTVFVTNAGNSLAADKAKQLTEWLG 69
G + VP V +G+ +AA +A++LT W+
Sbjct: 143 GEYGVPVALV--SGDDVAAREARELTPWIE 170
>gnl|CDD|233435 TIGR01488, HAD-SF-IB, Haloacid Dehalogenase superfamily, subfamily
IB, phosphoserine phosphatase-like. This model
represents a subfamily of the Haloacid Dehalogenase
superfamily of aspartate-nucleophile hydrolases.
Subfamily IA, B, C and D are distinguished from the rest
of the superfamily by the presence of a variable domain
between the first and second conserved catalytic motifs.
In subfamilies IA and IB, this domain consists of an
alpha-helical bundle. It was necessary to model these
two subfamilies separately, breaking them at a an
apparent phylogenetic bifurcation, so that the resulting
model(s) are not so broadly defined that members of
subfamily III (which lack the variable domain) are
included. Subfamily IA includes the enzyme phosphoserine
phosphatase (TIGR00338) as well as three hypothetical
equivalogs. Many members of these hypothetical
equivalogs have been annotated as PSPase-like or
PSPase-family proteins. In particular, the hypothetical
equivalog which appears to be most closely related to
PSPase contains only Archaea (while TIGR00338 contains
only eukaryotes and bacteria) of which some are
annotated as PSPases. Although this is a reasonable
conjecture, none of these sequences has sufficient
evidence for this assignment. If such should be found,
this model should be retired while the PSPase model
should be broadened to include these sequences [Unknown
function, Enzymes of unknown specificity].
Length = 177
Score = 26.2 bits (58), Expect = 8.8
Identities = 26/126 (20%), Positives = 43/126 (34%), Gaps = 25/126 (19%)
Query: 10 IFDIDGVLVRGKQVLPGVQDTFMNKLTNSGG---RFVVPTVFVTNAGNSLAADKAKQLTE 66
IFD DG L R QD+ ++ L G + T + S ++L
Sbjct: 3 IFDFDGTLTR--------QDSLIDLLAKLLGTNDEVIELTRLAPSGRISFEDALGRRLAL 54
Query: 67 WLGVEVEE------DQVVMSHTPIKMLHKYHTKH----TLISGQGPM---EEIAKRLGFN 113
EE + V + L + + ++SG G E +A++LG +
Sbjct: 55 LHRSRSEEVAKEFLARQVALRPGARELISWLKERGIDTVIVSG-GFDFFVEPVAEKLGID 113
Query: 114 KVVTVD 119
V
Sbjct: 114 DVFANR 119
>gnl|CDD|239102 cd02421, Peptidase_C39_likeD, A sub-family of peptidase family C39.
Peptidase family C39 mostly contains
bacteriocin-processing endopeptidases from bacteria. The
cysteine peptidases in family C39 cleave the
"double-glycine" leader peptides from the precursors of
various bacteriocins (mostly non-lantibiotic). The
cleavage is mediated by the transporter as part of the
secretion process. Bacteriocins are antibiotic proteins
secreted by some species of bacteria that inhibit the
growth of other bacterial species. The bacteriocin is
synthesized as a precursor with an N-terminal leader
peptide, and processing involves removal of the leader
peptide by cleavage at a Gly-Gly bond, followed by
translocation of the mature bacteriocin across the
cytoplasmic membrane. Most endopeptidases of family C39
are N-terminal domains in larger proteins (ABC
transporters) that serve both functions. The proposed
protease active site is not conserved in this
sub-family.
Length = 124
Score = 25.7 bits (57), Expect = 9.1
Identities = 19/52 (36%), Positives = 26/52 (50%), Gaps = 7/52 (13%)
Query: 112 FNKVVTVDSIRNAHPLLDCVDHRRRVSLFPRYCSRAQSLLSSELKITDRSLD 163
F K + DS+ PL D R +LFPR +RA LS+ ++ R LD
Sbjct: 19 FGKPASRDSLVAGLPL---DDGRLSPALFPRAAARAG--LSA--RVVRRPLD 63
>gnl|CDD|180395 PRK06091, PRK06091, membrane protein FdrA; Validated.
Length = 555
Score = 26.5 bits (59), Expect = 9.8
Identities = 15/46 (32%), Positives = 20/46 (43%), Gaps = 7/46 (15%)
Query: 52 AGNSLAADKAKQLTEWLGVEVEEDQVVMSHTPIKMLHKYHTKHTLI 97
G +LAA+ A L LGVE ++ H ML H +I
Sbjct: 338 TGGTLAAEAAGLLAGHLGVEADD-----EHHHGMMLD--ADGHQII 376
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
0.319 0.134 0.388
Gapped
Lambda K H
0.267 0.0879 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,092,819
Number of extensions: 816614
Number of successful extensions: 903
Number of sequences better than 10.0: 1
Number of HSP's gapped: 898
Number of HSP's successfully gapped: 42
Length of query: 183
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 92
Effective length of database: 6,901,388
Effective search space: 634927696
Effective search space used: 634927696
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 (21.8 bits)
S2: 56 (25.1 bits)