RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10860
(91 letters)
>gnl|CDD|163637 cd07394, MPP_Vps29, Homo sapiens Vps29 and related proteins,
metallophosphatase domain. Vps29 (vacuolar sorting
protein 29), also known as vacuolar membrane protein
Pep11, is a subunit of the retromer complex which is
responsible for the retrieval of mannose-6-phosphate
receptors (MPRs) from the endosomes for retrograde
transport back to the Golgi. Vps29 has a phosphoesterase
fold that acts as a protein interaction scaffold for
retromer complex assembly as well as a phosphatase with
specificity for the cytoplasmic tail of the MPR. The
retromer includes the following 5 subunits: Vps35,
Vps26, Vps29, and a dimer of the sorting nexins Vps5
(Snx1), and Vps17 (Snx2). Vps29 belongs to the
metallophosphatase (MPP) superfamily. MPPs are
functionally diverse, but all share a conserved domain
with an active site consisting of two metal ions
(usually manganese, iron, or zinc) coordinated with
octahedral geometry by a cage of histidine, aspartate,
and asparagine residues. The MPP superfamily includes:
Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat
debranching enzymes, YfcE-like phosphodiesterases,
purple acid phosphatases (PAPs), YbbF-like
UDP-2,3-diacylglucosamine hydrolases, and acid
sphingomyelinases (ASMases). The conserved domain is a
double beta-sheet sandwich with a di-metal active site
made up of residues located at the C-terminal side of
the sheets. This domain is thought to allow for
productive metal coordination.
Length = 178
Score = 163 bits (414), Expect = 4e-53
Identities = 61/79 (77%), Positives = 72/79 (91%)
Query: 3 GTSYPEKKVVTVGQFRIGLCHGHDIIPWGDPEALALLQRQLDVDILISGHTHKFEAYEHE 62
+YPE KV+TVGQF+IGL HGH ++PWGDP++LA LQRQLDVDILISGHTHKFEA+EHE
Sbjct: 65 NLNYPETKVITVGQFKIGLIHGHQVVPWGDPDSLAALQRQLDVDILISGHTHKFEAFEHE 124
Query: 63 NKFYINPGSATGAFNPLEP 81
KF+INPGSATGAF+PL+P
Sbjct: 125 GKFFINPGSATGAFSPLDP 143
>gnl|CDD|223695 COG0622, COG0622, Predicted phosphoesterase [General function
prediction only].
Length = 172
Score = 87.4 bits (217), Expect = 2e-23
Identities = 28/72 (38%), Positives = 37/72 (51%)
Query: 6 YPEKKVVTVGQFRIGLCHGHDIIPWGDPEALALLQRQLDVDILISGHTHKFEAYEHENKF 65
PE+ V+ VG +I L HGH D L L ++L D+LI GHTHK A +
Sbjct: 71 LPEELVLEVGGVKIFLTHGHLYFVKTDLSLLEYLAKELGADVLIFGHTHKPVAEKVGGIL 130
Query: 66 YINPGSATGAFN 77
+NPGS +G
Sbjct: 131 LVNPGSVSGPRG 142
>gnl|CDD|232794 TIGR00040, yfcE, phosphoesterase, MJ0936 family. Members of this
largely uncharacterized family share a motif
approximating DXH(X25)GDXXD(X25)GNHD as found in several
phosphoesterases, including the nucleases SbcD and
Mre11, and a family of uncharacterized archaeal putative
phosphoesterases described by TIGR00024. In this family,
the His residue in GNHD portion of the motif is not
conserved. The member MJ0936, one of two from
Methanococcus jannaschii, was shown (PMID:15128743) to
act on model phosphodiesterase substrates; a divalent
cation was required [Unknown function, Enzymes of
unknown specificity].
Length = 158
Score = 86.7 bits (215), Expect = 2e-23
Identities = 31/75 (41%), Positives = 38/75 (50%)
Query: 7 PEKKVVTVGQFRIGLCHGHDIIPWGDPEALALLQRQLDVDILISGHTHKFEAYEHENKFY 66
PE+++ GL HG + P GD L L ++L VD+LI GHTH A E
Sbjct: 69 PEEEIFEAEGIDFGLVHGDLVYPRGDLLVLEYLAKELGVDVLIFGHTHIPVAEELRGILL 128
Query: 67 INPGSATGAFNPLEP 81
INPGS TG N P
Sbjct: 129 INPGSLTGPRNGNTP 143
>gnl|CDD|221807 pfam12850, Metallophos_2, Calcineurin-like phosphoesterase
superfamily domain. Members of this family are part of
the Calcineurin-like phosphoesterase superfamily.
Length = 146
Score = 76.5 bits (189), Expect = 1e-19
Identities = 22/76 (28%), Positives = 32/76 (42%), Gaps = 2/76 (2%)
Query: 6 YPEKKVVTVGQFRIGLCHGHDIIPWGDPEALALLQRQLDVDILISGHTHKFEAYEHENKF 65
PE+ V+T+G FRI + HGH L ++ D++ GHTH +
Sbjct: 63 LPEELVLTLGGFRILVVHGHPYGVKHGLAELLA--KEGGADVVFFGHTHVPGVEKRGGTL 120
Query: 66 YINPGSATGAFNPLEP 81
+NPGS G
Sbjct: 121 LVNPGSVGGPRGGDPA 136
>gnl|CDD|163617 cd00841, MPP_YfcE, Escherichia coli YfcE and related proteins,
metallophosphatase domain. YfcE is a
manganase-dependent metallophosphatase, found in
bacteria and archaea, that cleaves bis-p-nitrophenyl
phosphate, thymidine 5'-monophosphate-p-nitrophenyl
ester, and p-nitrophenyl phosphorylcholine, but is
unable to hydrolyze 2',3 ' or 3',5' cyclic nucleic
phosphodiesters, and various phosphomonoesters,
including p-nitrophenyl phosphate. This family also
includes the Bacilus subtilis YsnB and Methanococcus
jannaschii MJ0936 proteins. This domain family belongs
to the metallophosphatase (MPP) superfamily. MPPs are
functionally diverse, but all share a conserved domain
with an active site consisting of two metal ions
(usually manganese, iron, or zinc) coordinated with
octahedral geometry by a cage of histidine, aspartate,
and asparagine residues. The MPP superfamily includes:
Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat
debranching enzymes, YfcE-like phosphodiesterases,
purple acid phosphatases (PAPs), YbbF-like
UDP-2,3-diacylglucosamine hydrolases, and acid
sphingomyelinases (ASMases). The conserved domain is a
double beta-sheet sandwich with a di-metal active site
made up of residues located at the C-terminal side of
the sheets. This domain is thought to allow for
productive metal coordination.
Length = 155
Score = 72.3 bits (178), Expect = 8e-18
Identities = 24/84 (28%), Positives = 36/84 (42%), Gaps = 4/84 (4%)
Query: 4 TSYPEKKVVTVGQFRIGLCHGHDIIPWGDPEALALLQRQLDVDILISGHTHKFEAYEHEN 63
PE+ V+ +G RI L HGH + L L ++ D+++ GHTH +
Sbjct: 63 PILPEEAVLEIGGKRIFLTHGHLYGVKNGLDRLYLA-KEGGADVVLYGHTHIPVIEKIGG 121
Query: 64 KFYINPGSATGAFNPLEPLNGRYA 87
+NPGS + P YA
Sbjct: 122 VLLLNPGSLSL---PRGGGPPTYA 142
>gnl|CDD|181869 PRK09453, PRK09453, phosphodiesterase; Provisional.
Length = 182
Score = 47.2 bits (113), Expect = 5e-08
Identities = 22/62 (35%), Positives = 28/62 (45%), Gaps = 7/62 (11%)
Query: 12 VTVGQFRIGLCHGHDIIPWGDPEALALLQRQLDVDILISGHTHKFEAYEHENKFYINPGS 71
V + R+ L HGH PE L L D D+L+ GHTH A + NPGS
Sbjct: 93 VLLEGKRLFLTHGHLY----GPENLPALH---DGDVLVYGHTHIPVAEKQGGIILFNPGS 145
Query: 72 AT 73
+
Sbjct: 146 VS 147
>gnl|CDD|163641 cd07398, MPP_YbbF-LpxH, Escherichia coli YbbF/LpxH and related
proteins, metallophosphatase domain. YbbF/LpxH is an
Escherichia coli UDP-2,3-diacylglucosamine hydrolase
thought to catalyze the fourth step of lipid A
biosynthesis, in which a precursor
UDP-2,3-diacylglucosamine is hydrolyzed to yield
2,3-diacylglucosamine 1-phosphate and UMP. YbbF belongs
to the metallophosphatase (MPP) superfamily. MPPs are
functionally diverse, but all share a conserved domain
with an active site consisting of two metal ions
(usually manganese, iron, or zinc) coordinated with
octahedral geometry by a cage of histidine, aspartate,
and asparagine residues. The MPP superfamily includes:
Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat
debranching enzymes, YfcE-like phosphodiesterases,
purple acid phosphatases (PAPs), YbbF-like
UDP-2,3-diacylglucosamine hydrolases, and acid
sphingomyelinases (ASMases). The conserved domain is a
double beta-sheet sandwich with a di-metal active site
made up of residues located at the C-terminal side of
the sheets. This domain is thought to allow for
productive metal coordination.
Length = 217
Score = 42.4 bits (100), Expect = 4e-06
Identities = 18/39 (46%), Positives = 24/39 (61%)
Query: 33 PEALALLQRQLDVDILISGHTHKFEAYEHENKFYINPGS 71
EA+A L R+ VD +I GHTH+ +E + K YIN G
Sbjct: 178 EEAVARLARRKGVDGVICGHTHRPALHELDGKLYINLGD 216
>gnl|CDD|215750 pfam00149, Metallophos, Calcineurin-like phosphoesterase. This
family includes a diverse range of phosphoesterases,
including protein phosphoserine phosphatases,
nucleotidases, sphingomyelin phosphodiesterases and
2'-3' cAMP phosphodiesterases as well as nucleases such
as bacterial SbcD or yeast MRE11. The most conserved
regions in this superfamily centre around the metal
chelating residues.
Length = 185
Score = 37.8 bits (87), Expect = 2e-04
Identities = 16/59 (27%), Positives = 23/59 (38%), Gaps = 8/59 (13%)
Query: 6 YPEKKVVTVGQFRIGLCHGH--------DIIPWGDPEALALLQRQLDVDILISGHTHKF 56
+ + +I L HG D I EAL L + VD+++ GHTH
Sbjct: 127 LDLLLLAALVDGKILLVHGPLSPSLDSGDDIYLFGEEALEDLLKDNGVDLVLRGHTHVP 185
>gnl|CDD|225460 COG2908, COG2908, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 237
Score = 36.9 bits (86), Expect = 5e-04
Identities = 15/39 (38%), Positives = 20/39 (51%)
Query: 33 PEALALLQRQLDVDILISGHTHKFEAYEHENKFYINPGS 71
P A+A R+ VD +I GHTH+ + YIN G
Sbjct: 176 PAAVADEARRHGVDGVIHGHTHRPAIHNIPGITYINLGD 214
>gnl|CDD|163614 cd00838, MPP_superfamily, metallophosphatase superfamily,
metallophosphatase domain. Metallophosphatases (MPPs),
also known as metallophosphoesterases,
phosphodiesterases (PDEs), binuclear
metallophosphoesterases, and dimetal-containing
phosphoesterases (DMPs), represent a diverse superfamily
of enzymes with a conserved domain containing an active
site consisting of two metal ions (usually manganese,
iron, or zinc) coordinated with octahedral geometry by a
cage of histidine, aspartate, and asparagine residues.
This superfamily includes: the phosphoprotein
phosphatases (PPPs), Mre11/SbcD-like exonucleases,
Dbr1-like RNA lariat debranching enzymes, YfcE-like
phosphodiesterases, purple acid phosphatases (PAPs),
YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid
sphingomyelinases (ASMases). The conserved domain is a
double beta-sheet sandwich with a di-metal active site
made up of residues located at the C-terminal side of
the sheets. This domain is thought to allow for
productive metal coordination.
Length = 131
Score = 32.7 bits (74), Expect = 0.008
Identities = 18/43 (41%), Positives = 23/43 (53%), Gaps = 2/43 (4%)
Query: 30 WGDPEALALLQRQLDVDILISGHTHKFEAYEH--ENKFYINPG 70
EAL L + VD+++SGHTH +E E YINPG
Sbjct: 89 DPGSEALLELLEKYGVDLVLSGHTHVYERREPDGGGTLYINPG 131
>gnl|CDD|163628 cd07385, MPP_YkuE_C, Bacillus subtilis YkuE and related proteins,
C-terminal metallophosphatase domain. YkuE is an
uncharacterized Bacillus subtilis protein with a
C-terminal metallophosphatase domain and an N-terminal
twin-arginine (RR) motif. An RR-signal peptide derived
from the Bacillus subtilis YkuE protein can direct
Tat-dependent secretion of agarase in Streptomyces
lividans. This is an indication that YkuE is transported
by the Bacillus subtilis Tat (Twin-arginine
translocation) pathway machinery. YkuE belongs to the
metallophosphatase (MPP) superfamily. MPPs are
functionally diverse, but all share a conserved domain
with an active site consisting of two metal ions
(usually manganese, iron, or zinc) coordinated with
octahedral geometry by a cage of histidine, aspartate,
and asparagine residues. The MPP superfamily includes:
Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat
debranching enzymes, YfcE-like phosphodiesterases,
purple acid phosphatases (PAPs), YbbF-like
UDP-2,3-diacylglucosamine hydrolases, and acid
sphingomyelinases (ASMases). The conserved domain is a
double beta-sheet sandwich with a di-metal active site
made up of residues located at the C-terminal side of
the sheets. This domain is thought to allow for
productive metal coordination.
Length = 223
Score = 32.3 bits (74), Expect = 0.017
Identities = 11/40 (27%), Positives = 14/40 (35%), Gaps = 9/40 (22%)
Query: 15 GQFRIGLCHGHDIIPWGDPEALALLQRQLDVDILISGHTH 54
I L H P+ VD+ +SGHTH
Sbjct: 134 DDPNILLAH--------QPDTAEEAAA-WGVDLQLSGHTH 164
>gnl|CDD|163653 cd07410, MPP_CpdB_N, Escherichia coli CpdB and related proteins,
N-terminal metallophosphatase domain. CpdB is a
bacterial periplasmic protein with an N-terminal
metallophosphatase domain and a C-terminal
3'-nucleotidase domain. This alignment model represents
the N-terminal metallophosphatase domain, which has
2',3'-cyclic phosphodiesterase activity, hydrolyzing the
2',3'-cyclic phosphates of adenosine, guanosine,
cytosine and uridine to yield nucleoside and phosphate.
CpdB also hydrolyzes the chromogenic substrates
p-nitrophenyl phosphate (PNPP), bis(PNPP) and
p-nitrophenyl phosphorylcholine (NPPC). CpdB is thought
to play a scavenging role during RNA hydrolysis by
converting the non-transportable nucleotides produced by
RNaseI to nucleosides which can easily enter a cell for
use as a carbon source. This family also includes YfkN,
a Bacillus subtilis nucleotide phosphoesterase with two
copies of each of the metallophosphatase and
3'-nucleotidase domains. The N-terminal
metallophosphatase domain belongs to a large superfamily
of distantly related metallophosphatases (MPPs) that
includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA
lariat debranching enzymes, YfcE-like
phosphodiesterases, purple acid phosphatases (PAPs),
YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid
sphingomyelinases (ASMases). MPPs are functionally
diverse, but all share a conserved domain with an active
site consisting of two metal ions (usually manganese,
iron, or zinc) coordinated with octahedral geometry by a
cage of histidine, aspartate, and asparagine residues.
The conserved domain is a double beta-sheet sandwich
with a di-metal active site made up of residues located
at the C-terminal side of the sheets. This domain is
thought to allow for productive metal coordination.
Length = 277
Score = 32.1 bits (74), Expect = 0.021
Identities = 11/42 (26%), Positives = 19/42 (45%), Gaps = 5/42 (11%)
Query: 19 IGLCHG---HDIIPWGDPE--ALALLQRQLDVDILISGHTHK 55
+ L HG D+ E A L + +D +++GH H+
Sbjct: 188 VVLAHGGFERDLEESLTGENAAYELAEEVPGIDAILTGHQHR 229
>gnl|CDD|152302 pfam11866, DUF3386, Protein of unknown function (DUF3386). This
family of proteins are functionally uncharacterized.
This protein is found in bacteria and eukaryotes.
Proteins in this family are about 220 amino acids in
length.
Length = 214
Score = 31.1 bits (71), Expect = 0.037
Identities = 18/71 (25%), Positives = 30/71 (42%), Gaps = 1/71 (1%)
Query: 5 SYPEKKVVTVGQFRIGLCHGHDIIPWGDPEALALLQRQLDVDILISGHTHKFEAYEHENK 64
++ + GQFR+G ++ D E L + QL ++ I FE +N
Sbjct: 33 TWSDGDKSVEGQFRVGADLKAKVLGIEDEEVLKAIYSQLW-EVAIHRVRRSFEETHGKNT 91
Query: 65 FYINPGSATGA 75
F + A+GA
Sbjct: 92 FTLGETDASGA 102
>gnl|CDD|224326 COG1408, COG1408, Predicted phosphohydrolases [General function
prediction only].
Length = 284
Score = 30.5 bits (69), Expect = 0.068
Identities = 16/46 (34%), Positives = 20/46 (43%), Gaps = 9/46 (19%)
Query: 9 KKVVTVGQFRIGLCHGHDIIPWGDPEALALLQRQLDVDILISGHTH 54
K + I L H DII L R VD+++SGHTH
Sbjct: 186 LKQLDEDLPGILLSHEPDII---------LQLRLYGVDLVLSGHTH 222
>gnl|CDD|235420 PRK05340, PRK05340, UDP-2,3-diacylglucosamine hydrolase;
Provisional.
Length = 241
Score = 30.2 bits (69), Expect = 0.084
Identities = 13/23 (56%), Positives = 16/23 (69%)
Query: 33 PEALALLQRQLDVDILISGHTHK 55
PEA+A L + VD LI GHTH+
Sbjct: 176 PEAVAALMEKHGVDTLIHGHTHR 198
>gnl|CDD|163655 cd07412, MPP_YhcR_N, Bacillus subtilis YhcR endonuclease and
related proteins, N-terminal metallophosphatase domain.
YhcR is a Bacillus subtilis sugar-nonspecific
endonuclease. It cleaves endonucleolytically to yield
nucleotide 3'-monophosphate products, similar to
Staphylococcus aureus micrococcal nuclease. YhcR appears
to be located in the cell wall, and is thought to be a
substrate for a Bacillus subtilis sortase. YhcR is the
major calcium-activated nuclease of B. subtilis. The
N-terminal metallophosphatase domain belongs to a large
superfamily of distantly related metallophosphatases
(MPPs) that includes: Mre11/SbcD-like exonucleases,
Dbr1-like RNA lariat debranching enzymes, YfcE-like
phosphodiesterases, purple acid phosphatases (PAPs),
YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid
sphingomyelinases (ASMases). MPPs are functionally
diverse, but all share a conserved domain with an active
site consisting of two metal ions (usually manganese,
iron, or zinc) coordinated with octahedral geometry by a
cage of histidine, aspartate, and asparagine residues.
The conserved domain is a double beta-sheet sandwich
with a di-metal active site made up of residues located
at the C-terminal side of the sheets. This domain is
thought to allow for productive metal coordination.
Length = 288
Score = 30.0 bits (68), Expect = 0.100
Identities = 7/21 (33%), Positives = 11/21 (52%)
Query: 44 DVDILISGHTHKFEAYEHENK 64
DVD++ +GHTH+
Sbjct: 229 DVDVVFAGHTHQAYNCTVPAG 249
>gnl|CDD|163640 cd07397, MPP_DevT, Myxococcus xanthus DevT and related proteins,
metallophosphatase domain. DevT is a component in the
C-signal response pathway in Myxococcus xanthus that
stimulates the developmentally regulated expression of
the FruA response regulator protein and is required for
methylation of FrzCD during fruiting body formation.
DevT mutants having an in-frame deletion in the devT
gene, display delayed aggregation and a cell autonomous
sporulation defect. DevT belongs to the
metallophosphatase (MPP) superfamily. MPPs are
functionally diverse, but all share a conserved domain
with an active site consisting of two metal ions
(usually manganese, iron, or zinc) coordinated with
octahedral geometry by a cage of histidine, aspartate,
and asparagine residues. The MPP superfamily includes:
Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat
debranching enzymes, YfcE-like phosphodiesterases,
purple acid phosphatases (PAPs), YbbF-like
UDP-2,3-diacylglucosamine hydrolases, and acid
sphingomyelinases (ASMases). The conserved domain is a
double beta-sheet sandwich with a di-metal active site
made up of residues located at the C-terminal side of
the sheets. This domain is thought to allow for
productive metal coordination.
Length = 238
Score = 29.6 bits (67), Expect = 0.13
Identities = 10/29 (34%), Positives = 17/29 (58%), Gaps = 3/29 (10%)
Query: 30 WGDP---EALALLQRQLDVDILISGHTHK 55
WGDP A++ +Q+ V +++ GH H
Sbjct: 179 WGDPDLALAISQIQQGRQVPLVVFGHMHH 207
>gnl|CDD|200419 TIGR04168, TIGR04168, TIGR04168 family protein. Members of this
uncharacterized protein family are restricted, in 49 of
50 genomes, to organisms with a family TIGR04167 radical
SAM protein, which occasionally is a selenoprotein.
Length = 269
Score = 29.5 bits (67), Expect = 0.18
Identities = 9/28 (32%), Positives = 17/28 (60%), Gaps = 3/28 (10%)
Query: 30 WGDP---EALALLQRQLDVDILISGHTH 54
WGDP A+A +++ + +++ GH H
Sbjct: 167 WGDPDLALAIAQIRKLKQIPLVVFGHMH 194
>gnl|CDD|224230 COG1311, HYS2, Archaeal DNA polymerase II, small subunit/DNA
polymerase delta, subunit B [DNA replication,
recombination, and repair].
Length = 481
Score = 28.5 bits (64), Expect = 0.35
Identities = 9/26 (34%), Positives = 14/26 (53%)
Query: 46 DILISGHTHKFEAYEHENKFYINPGS 71
D+ +GH HKF +E +N G+
Sbjct: 420 DVFHTGHVHKFGTGVYEGVNLVNSGT 445
>gnl|CDD|238152 cd00248, Mth938-like, Mth938-like domain. The members of this
family include: Mth938, 2P1, Xcr35, Rpa2829, and
several uncharacterized sequences. Mth938 is a
hypothetical protein encoded by the Methanobacterium
thermoautotrophicum (Mth) genome. This protein
crystallizes as a dimer, although it is monomeric in
solution, with one disulfide bond in each monomer. 2P1
is a partially characterized nuclear protein which is
homologous to E3-3 from rat and known to be alternately
spliced. Xcr35 and Rpa2829 are hypothetical proteins of
unknown function from the Xanthomonas campestris and
Rhodopseudomonas palustris genomes, respectively, for
which the crystal structures have been determined.
Length = 109
Score = 28.0 bits (63), Expect = 0.39
Identities = 18/60 (30%), Positives = 23/60 (38%), Gaps = 17/60 (28%)
Query: 15 GQFRIG--------LCHGHDIIPWG-------DPEALALLQRQLDVDILI--SGHTHKFE 57
G FRI L ++PW DPEAL L + DIL+ +G F
Sbjct: 8 GGFRIAGQVYRGPLLVLPDGVVPWDGTSLSDLDPEALLPLLAEDRPDILLIGTGAEIAFL 67
>gnl|CDD|163643 cd07400, MPP_YydB, Bacillus subtilis YydB and related proteins,
metallophosphatase domain. YydB (BSU40220) is an
uncharacterized Bacillus subtilis protein that belongs
to the following Bacillus subtilis gene cluster
yydB-yydC-yydD-yydG-yydH-yydI-yydJ. YydB belongs to the
metallophosphatase (MPP) superfamily. MPPs are
functionally diverse, but all share a conserved domain
with an active site consisting of two metal ions
(usually manganese, iron, or zinc) coordinated with
octahedral geometry by a cage of histidine, aspartate,
and asparagine residues. The MPP superfamily includes:
Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat
debranching enzymes, YfcE-like phosphodiesterases,
purple acid phosphatases (PAPs), YbbF-like
UDP-2,3-diacylglucosamine hydrolases, and acid
sphingomyelinases (ASMases). The conserved domain is a
double beta-sheet sandwich with a di-metal active site
made up of residues located at the C-terminal side of
the sheets. This domain is thought to allow for
productive metal coordination.
Length = 144
Score = 28.1 bits (63), Expect = 0.42
Identities = 12/64 (18%), Positives = 18/64 (28%), Gaps = 11/64 (17%)
Query: 19 IGLCHGH-------DIIPWGDPEALALLQRQLDVDILISGHTHKFEAYEHENK----FYI 67
I + H D L + VD+++ GH H N I
Sbjct: 81 IVVLHHPLVPPPGSGRERLLDAGDALKLLAEAGVDLVLHGHKHVPYVGNISNAGGGLVVI 140
Query: 68 NPGS 71
G+
Sbjct: 141 GAGT 144
>gnl|CDD|204415 pfam10212, TTKRSYEDQ, Predicted coiled-coil domain-containing
protein. This is the C-terminal 500 amino acids of a
family of proteins with a predicted coiled-coil domain
conserved from nematodes to humans. It carries a
characteristic TTKRSYEDQ sequence-motif. The function
is not known.
Length = 518
Score = 28.3 bits (63), Expect = 0.49
Identities = 10/21 (47%), Positives = 11/21 (52%)
Query: 49 ISGHTHKFEAYEHENKFYINP 69
IS KF Y HEN Y+ P
Sbjct: 39 ISPLNQKFSQYLHENAAYVRP 59
>gnl|CDD|163616 cd00840, MPP_Mre11_N, Mre11 nuclease, N-terminal metallophosphatase
domain. Mre11 (also known as SbcD in Escherichia coli)
is a subunit of the MRX protein complex. This complex
includes: Mre11, Rad50, and Xrs2/Nbs1, and plays a vital
role in several nuclear processes including DNA
double-strand break repair, telomere length maintenance,
cell cycle checkpoint control, and meiotic
recombination, in eukaryotes. During double-strand
break repair, the MRX complex is required to hold the
two ends of a broken chromosome together. In vitro
studies show that Mre11 has 3'-5' exonuclease activity
on dsDNA templates and endonuclease activity on dsDNA
and ssDNA templates. In addition to the N-terminal
phosphatase domain, the eukaryotic MRE11 members of this
family have a C-terminal DNA binding domain (not
included in this alignment model). MRE11-like proteins
are found in prokaryotes and archaea was well as in
eukaryotes. Mre11 belongs to the metallophosphatase
(MPP) superfamily. MPPs are functionally diverse, but
all share a conserved domain with an active site
consisting of two metal ions (usually manganese, iron,
or zinc) coordinated with octahedral geometry by a cage
of histidine, aspartate, and asparagine residues. The
MPP superfamily includes: Mre11/SbcD-like exonucleases,
Dbr1-like RNA lariat debranching enzymes, YfcE-like
phosphodiesterases, purple acid phosphatases (PAPs),
YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid
sphingomyelinases (ASMases). The conserved domain is a
double beta-sheet sandwich with a di-metal active site
made up of residues located at the C-terminal side of
the sheets. This domain is thought to allow for
productive metal coordination.
Length = 223
Score = 27.7 bits (62), Expect = 0.65
Identities = 15/61 (24%), Positives = 21/61 (34%), Gaps = 4/61 (6%)
Query: 15 GQFRIGLCHGH--DIIPWGDPEALALLQRQLD--VDILISGHTHKFEAYEHENKFYINPG 70
F I L HG P A + + L D + GH H+ + + PG
Sbjct: 156 DDFNILLLHGGVAGAGPSDSERAPFVPEALLPAGFDYVALGHIHRPQIILGGGPPIVYPG 215
Query: 71 S 71
S
Sbjct: 216 S 216
>gnl|CDD|163639 cd07396, MPP_Nbla03831, Homo sapiens Nbla03831 and related
proteins, metallophosphatase domain. Nbla03831 (also
known as LOC56985) is an uncharacterized Homo sapiens
protein with a domain that belongs to the
metallophosphatase (MPP) superfamily. MPPs are
functionally diverse, but all share a conserved domain
with an active site consisting of two metal ions
(usually manganese, iron, or zinc) coordinated with
octahedral geometry by a cage of histidine, aspartate,
and asparagine residues. The MPP superfamily includes:
Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat
debranching enzymes, YfcE-like phosphodiesterases,
purple acid phosphatases (PAPs), YbbF-like
UDP-2,3-diacylglucosamine hydrolases, and acid
sphingomyelinases (ASMases). The conserved domain is a
double beta-sheet sandwich with a di-metal active site
made up of residues located at the C-terminal side of
the sheets. This domain is thought to allow for
productive metal coordination.
Length = 267
Score = 27.6 bits (62), Expect = 0.79
Identities = 10/26 (38%), Positives = 14/26 (53%)
Query: 30 WGDPEALALLQRQLDVDILISGHTHK 55
W E L++L+ V ISGH H+
Sbjct: 202 WNHEEVLSILRAYGCVKACISGHDHE 227
>gnl|CDD|184118 PRK13531, PRK13531, regulatory ATPase RavA; Provisional.
Length = 498
Score = 27.3 bits (61), Expect = 0.92
Identities = 10/23 (43%), Positives = 16/23 (69%), Gaps = 2/23 (8%)
Query: 30 WGDPEALALLQRQLDVDILISGH 52
W D ++L LLQ+QL + L++ H
Sbjct: 285 WHDAQSLNLLQQQL--EQLMTEH 305
>gnl|CDD|185607 PTZ00422, PTZ00422, glideosome-associated protein 50; Provisional.
Length = 394
Score = 27.1 bits (60), Expect = 1.2
Identities = 12/37 (32%), Positives = 17/37 (45%)
Query: 39 LQRQLDVDILISGHTHKFEAYEHENKFYINPGSATGA 75
L + VD+ ISG+ E E +IN GS +
Sbjct: 243 LLKDAQVDLYISGYDRNMEVLTDEGTAHINCGSGGNS 279
>gnl|CDD|236505 PRK09419, PRK09419, bifunctional 2',3'-cyclic nucleotide
2'-phosphodiesterase/3'-nucleotidase precursor protein;
Reviewed.
Length = 1163
Score = 27.1 bits (60), Expect = 1.5
Identities = 10/24 (41%), Positives = 14/24 (58%)
Query: 31 GDPEALALLQRQLDVDILISGHTH 54
G+ L L ++ VD +IS HTH
Sbjct: 857 GEITGLELAKKVKGVDAIISAHTH 880
>gnl|CDD|163654 cd07411, MPP_SoxB_N, Thermus thermophilus SoxB and related
proteins, N-terminal metallophosphatase domain. SoxB
(sulfur oxidation protein B) is a periplasmic
thiosulfohydrolase and an essential component of the
sulfur oxidation pathway in archaea and bacteria. SoxB
has a dinuclear manganese cluster and is thought to
catalyze the release of sulfate from a protein-bound
cysteine S-thiosulfonate. SoxB is expressed from the
sox (sulfur oxidation) gene cluster, which encodes 15
other sox genes, and has two domains, an N-terminal
metallophosphatase domain and a C-terminal
5'-nucleotidase domain. SoxB binds the SoxYZ complex
and is thought to function as a sulfate-thiohydrolase.
SoxB is closely related to the UshA, YchR, and CpdB
proteins, all of which have the same two-domain
architecture. The N-terminal metallophosphatase domain
belongs to a large superfamily of distantly related
metallophosphatases (MPPs) that includes:
Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat
debranching enzymes, YfcE-like phosphodiesterases,
purple acid phosphatases (PAPs), YbbF-like
UDP-2,3-diacylglucosamine hydrolases, and acid
sphingomyelinases (ASMases). MPPs are functionally
diverse, but all share a conserved domain with an active
site consisting of two metal ions (usually manganese,
iron, or zinc) coordinated with octahedral geometry by a
cage of histidine, aspartate, and asparagine residues.
The conserved domain is a double beta-sheet sandwich
with a di-metal active site made up of residues located
at the C-terminal side of the sheets. This domain is
thought to allow for productive metal coordination.
Length = 264
Score = 26.8 bits (60), Expect = 1.7
Identities = 10/24 (41%), Positives = 16/24 (66%)
Query: 31 GDPEALALLQRQLDVDILISGHTH 54
G P + L +R +D+++SGHTH
Sbjct: 194 GLPVDVELAERVPGIDVILSGHTH 217
>gnl|CDD|215511 PLN02949, PLN02949, transferase, transferring glycosyl groups.
Length = 463
Score = 26.6 bits (59), Expect = 1.8
Identities = 12/40 (30%), Positives = 18/40 (45%), Gaps = 6/40 (15%)
Query: 8 EKKVVTVGQFRIGLCHGHDIIPWGDPEALALLQRQLDVDI 47
+++V QFR H + EA AL +LD D+
Sbjct: 268 PPYIISVAQFRPEKAHALQL------EAFALALEKLDADV 301
>gnl|CDD|113530 pfam04763, DUF562, Protein of unknown function (DUF562). Family
of uncharacterized proteins.
Length = 146
Score = 26.2 bits (58), Expect = 2.0
Identities = 11/36 (30%), Positives = 15/36 (41%), Gaps = 6/36 (16%)
Query: 8 EKKVVTVGQFRIGLCHGHDIIPWGDPEALALLQRQL 43
EK VV V H PE+++LL +L
Sbjct: 15 EKNVVVV------CNHSTPGPESLPPESVSLLIEEL 44
>gnl|CDD|233600 TIGR01854, lipid_A_lpxH, UDP-2,3-diacylglucosamine hydrolase. This
model represents LpxH, UDP-2,3-diacylglucosamine
hydrolase, and essential enzyme in E. coli that
catalyzes the fourth step in lipid A biosynthesis. Note
that Pseudomonas aeruginosa has both a member of this
family that shares this function and a more distant
homolog, designated LpxH2, that does not. Many species
that produce lipid A lack an lpxH gene in this family;
some of those species have an lpxH2 gene instead,
although for which the function is unknown [Cell
envelope, Biosynthesis and degradation of surface
polysaccharides and lipopolysaccharides].
Length = 231
Score = 26.2 bits (58), Expect = 2.1
Identities = 12/31 (38%), Positives = 16/31 (51%), Gaps = 1/31 (3%)
Query: 33 PEALALLQRQLDVDILISGHTHKFEAYEHEN 63
P +A + R+ VD LI GHTH+ A
Sbjct: 174 PAEVAAVMRRYGVDRLIHGHTHR-PAIHPLQ 203
>gnl|CDD|240622 cd05198, formate_dh_like, Formate/glycerate and related
dehydrogenases of the D-specific 2-hydroxy acid
dehydrogenase family. Formate dehydrogenase,
D-specific 2-hydroxy acid dehydrogenase,
Phosphoglycerate Dehydrogenase, Lactate dehydrogenase,
Thermostable Phosphite Dehydrogenase, and
Hydroxy(phenyl)pyruvate reductase, among others, share
a characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form.
2-hydroxyacid dehydrogenases are enzymes that catalyze
the conversion of a wide variety of D-2-hydroxy acids
to their corresponding keto acids. The general
mechanism is (R)-lactate + acceptor to pyruvate +
reduced acceptor. The NAD+ binding domain is inserted
within the linear sequence of the mostly N-terminal
catalytic domain, which has a similar domain structure
to the internal NAD binding domain. Structurally, these
domains are connected by extended alpha helices and
create a cleft in which NAD is bound, primarily to the
C-terminal portion of the 2nd (internal) domain. Some
related proteins have similar structural subdomain but
with a tandem arrangement of the catalytic and
NAD-binding subdomains in the linear sequence. Formate
dehydrogenase (FDH) catalyzes the NAD+-dependent
oxidation of formate ion to carbon dioxide with the
concomitant reduction of NAD+ to NADH. FDHs of this
family contain no metal ions or prosthetic groups.
Catalysis occurs though direct transfer of hydride ion
to NAD+ without the stages of acid-base catalysis
typically found in related dehydrogenases. FDHs are
found in all methylotrophic microorganisms in energy
production and in the stress responses of plants.
Formate/glycerate and related dehydrogenases of the
D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-Adenosylhomocysteine Hydrolase, among others. While
many members of this family are dimeric, alanine DH is
hexameric and phosphoglycerate DH is tetrameric.
Length = 302
Score = 26.4 bits (59), Expect = 2.1
Identities = 10/33 (30%), Positives = 12/33 (36%)
Query: 23 HGHDIIPWGDPEALALLQRQLDVDILISGHTHK 55
G ++I D A L D D LI T
Sbjct: 20 TGFEVIVADDLLADELEALLADADALIVSSTTP 52
>gnl|CDD|163645 cd07402, MPP_GpdQ, Enterobacter aerogenes GpdQ and related
proteins, metallophosphatase domain. GpdQ
(glycerophosphodiesterase Q, also known as Rv0805 in
Mycobacterium tuberculosis) is a binuclear
metallophosphoesterase from Enterobacter aerogenes that
catalyzes the hydrolysis of mono-, di-, and triester
substrates, including some organophosphate pesticides
and products of the degradation of nerve agents. The
GpdQ homolog, Rv0805, has 2',3'-cyclic nucleotide
phosphodiesterase activity. GpdQ and Rv0805 belong to
the metallophosphatase (MPP) superfamily. MPPs are
functionally diverse, but all share a conserved domain
with an active site consisting of two metal ions
(usually manganese, iron, or zinc) coordinated with
octahedral geometry by a cage of histidine, aspartate,
and asparagine residues. The MPP superfamily includes:
Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat
debranching enzymes, YfcE-like phosphodiesterases,
purple acid phosphatases (PAPs), YbbF-like
UDP-2,3-diacylglucosamine hydrolases, and acid
sphingomyelinases (ASMases). The conserved domain is a
double beta-sheet sandwich with a di-metal active site
made up of residues located at the C-terminal side of
the sheets. This domain is thought to allow for
productive metal coordination.
Length = 240
Score = 26.0 bits (58), Expect = 3.0
Identities = 14/39 (35%), Positives = 20/39 (51%), Gaps = 2/39 (5%)
Query: 17 FRIGLCHGHDIIPWGDPEAL-ALLQRQLDVDILISGHTH 54
F +G D I + EAL A+L R +V ++ GH H
Sbjct: 155 FPVG-IAWMDAIGLRNAEALAAVLARHPNVRAILCGHVH 192
>gnl|CDD|201648 pfam01188, MR_MLE, Mandelate racemase / muconate lactonizing
enzyme, C-terminal domain. C-terminal domain is TIM
barrel fold, dehydratase-like domain. Manganese is
associated with this domain.
Length = 69
Score = 24.7 bits (55), Expect = 3.1
Identities = 8/20 (40%), Positives = 11/20 (55%)
Query: 28 IPWGDPEALALLQRQLDVDI 47
+P D E LA L+R + I
Sbjct: 47 LPPDDLEGLAELRRATPIPI 66
>gnl|CDD|239432 cd03316, MR_like, Mandelate racemase (MR)-like subfamily of the
enolase superfamily. Enzymes of this subgroup share
three conserved carboxylate ligands for the essential
divalent metal ion (usually Mg2+), two aspartates and a
glutamate, and conserved catalytic residues, a
Lys-X-Lys motif and a conserved histidine-aspartate
dyad. Members of the MR subgroup are mandelate racemase,
D-glucarate/L-idarate dehydratase (GlucD),
D-altronate/D-mannonate dehydratase , D-galactonate
dehydratase (GalD) , D-gluconate dehydratase (GlcD), and
L-rhamnonate dehydratase (RhamD).
Length = 357
Score = 25.7 bits (57), Expect = 3.4
Identities = 8/22 (36%), Positives = 12/22 (54%)
Query: 26 DIIPWGDPEALALLQRQLDVDI 47
+ +P D E LA L++ V I
Sbjct: 222 EPVPPDDLEGLARLRQATSVPI 243
>gnl|CDD|184948 PRK14986, PRK14986, glycogen phosphorylase; Provisional.
Length = 815
Score = 25.9 bits (57), Expect = 3.5
Identities = 8/18 (44%), Positives = 12/18 (66%), Gaps = 2/18 (11%)
Query: 72 ATGAFNPLEPLNGRYANV 89
+G F+P EP GRY ++
Sbjct: 728 GSGVFSPEEP--GRYRDL 743
>gnl|CDD|163634 cd07391, MPP_PF1019, Pyrococcus furiosus PF1019 and related
proteins, metallophosphatase domain. This family
includes bacterial and archeal proteins homologous to
PF1019, an uncharacterized Pyrococcus furiosus protein.
The domain present in members of this family belongs to
the metallophosphatase (MPP) superfamily. MPPs are
functionally diverse, but all share a conserved domain
with an active site consisting of two metal ions
(usually manganese, iron, or zinc) coordinated with
octahedral geometry by a cage of histidine, aspartate,
and asparagine residues. The MPP superfamily includes:
Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat
debranching enzymes, YfcE-like phosphodiesterases,
purple acid phosphatases (PAPs), YbbF-like
UDP-2,3-diacylglucosamine hydrolases, and acid
sphingomyelinases (ASMases). The conserved domain is a
double beta-sheet sandwich with a di-metal active site
made up of residues located at the C-terminal side of
the sheets. This domain is thought to allow for
productive metal coordination.
Length = 172
Score = 25.7 bits (57), Expect = 3.5
Identities = 13/52 (25%), Positives = 18/52 (34%), Gaps = 15/52 (28%)
Query: 6 YPEKKVVTVGQFRIG---LCHGHDIIPWGDPEALALLQRQLDVDILISGHTH 54
+ V V +G HGH P LD +++I GH H
Sbjct: 93 LKDLNVEVVEGLLLGGFLFFHGHKPPP------------PLDAELVIIGHEH 132
>gnl|CDD|224809 COG1897, MetA, Homoserine trans-succinylase [Amino acid transport
and metabolism].
Length = 307
Score = 25.8 bits (57), Expect = 3.5
Identities = 11/26 (42%), Positives = 14/26 (53%), Gaps = 1/26 (3%)
Query: 42 QLDVDIL-ISGHTHKFEAYEHENKFY 66
Q+D+ +L I H K EH N FY
Sbjct: 64 QVDITLLRIDSHESKNTPAEHLNSFY 89
>gnl|CDD|223867 COG0796, MurI, Glutamate racemase [Cell envelope biogenesis, outer
membrane].
Length = 269
Score = 25.6 bits (57), Expect = 3.6
Identities = 15/57 (26%), Positives = 23/57 (40%), Gaps = 12/57 (21%)
Query: 31 GDPEALALLQRQL------DVDILISGHTH------KFEAYEHENKFYINPGSATGA 75
G P AL +L+ L D L+ G TH + + E+ I+ G+ T
Sbjct: 158 GGPVALEVLKEYLPPLQEAGPDTLVLGCTHYPLLKPEIQQVLGEHVALIDSGAETAR 214
>gnl|CDD|163652 cd07409, MPP_CD73_N, CD73 ecto-5'-nucleotidase and related
proteins, N-terminal metallophosphatase domain. CD73 is
a mammalian ecto-5'-nucleotidase expressed in
endothelial cells and lymphocytes that catalyzes the
conversion of 5'-AMP to adenosine in the final step of a
pathway that generates adenosine from ATP. This pathway
also includes a CD39 nucleoside triphosphate
dephosphorylase that mediates the dephosphorylation of
ATP to ADP and then to 5'-AMP. These enzymes all have
an N-terminal metallophosphatase domain and a C-terminal
5'nucleotidase domain. The N-terminal
metallophosphatase domain belongs to a large superfamily
of distantly related metallophosphatases (MPPs) that
includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA
lariat debranching enzymes, YfcE-like
phosphodiesterases, purple acid phosphatases (PAPs),
YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid
sphingomyelinases (ASMases). MPPs are functionally
diverse, but all share a conserved domain with an active
site consisting of two metal ions (usually manganese,
iron, or zinc) coordinated with octahedral geometry by a
cage of histidine, aspartate, and asparagine residues.
The conserved domain is a double beta-sheet sandwich
with a di-metal active site made up of residues located
at the C-terminal side of the sheets. This domain is
thought to allow for productive metal coordination.
Length = 281
Score = 25.6 bits (57), Expect = 3.6
Identities = 6/13 (46%), Positives = 10/13 (76%)
Query: 44 DVDILISGHTHKF 56
VD+++ GH+H F
Sbjct: 206 GVDVIVGGHSHTF 218
>gnl|CDD|238927 cd01965, Nitrogenase_MoFe_beta_like, Nitrogenase_MoFe_beta_like:
Nitrogenase MoFe protein, beta subunit_like. The
nitrogenase enzyme catalyzes the ATP-dependent reduction
of dinitrogen (N2) to ammonia. This group contains the
beta subunits of component 1 of the three known
genetically distinct types of nitrogenase systems: a
molybdenum-dependent nitrogenase (Mo-nitrogenase), a
vanadium-dependent nitrogenase (V-nitrogenase), and an
iron-only nitrogenase (Fe-nitrogenase). These
nitrogenase systems consist of component 1 (MoFe
protein, VFe protein or, FeFe protein respectively) and,
component 2 (Fe protein). The most widespread and best
characterized of these systems is the Mo-nitrogenase.
MoFe is an alpha2beta2 tetramer, the alternative
nitrogenases are alpha2beta2delta2 hexamers having
alpha and beta subunits similar to the alpha and beta
subunits of MoFe. For MoFe, each alphabeta pair contains
one P-cluster (at the alphabeta interface) and, one
molecule of iron molybdenum cofactor (FeMoco) contained
within the alpha subunit. The Fe protein contains, a
single [4Fe-4S] cluster from which electrons are
transferred to the P-cluster of the MoFe and in turn,
to FeMoCo, the site of substrate reduction. The
V-nitrogenase requires an iron-vanadium cofactor
(FeVco), the iron only-nitrogenase an iron only cofactor
(FeFeco). These cofactors are analogous to the FeMoco.
The V-nitrogenase has P clusters identical to those of
MoFe. In addition to N2, nitrogenase also catalyzes the
reduction of a variety of other substrates such as
acetylene The V-nitrogenase differs from the
Mo-nitrogenase in that it produces free hydrazine, as a
minor product during N2-reduction and, ethane as a minor
product during acetylene reduction.
Length = 428
Score = 25.6 bits (57), Expect = 3.9
Identities = 10/45 (22%), Positives = 19/45 (42%), Gaps = 1/45 (2%)
Query: 23 HGHDIIPWGDPEALALLQRQLDVDILISGHTHKFEAYEHENKFYI 67
+++ GD L L ++ VD+LI G++H +
Sbjct: 350 IPAEVVFVGDLWDLESLAKEEPVDLLI-GNSHGRYLARDLGIPLV 393
>gnl|CDD|163629 cd07386, MPP_DNA_pol_II_small_archeal_C, archeal DNA polymerase II,
small subunit, C-terminal metallophosphatase domain.
The small subunit of the archeal DNA polymerase II
contains a C-terminal metallophosphatase domain. This
domain is thought to be functionally active because the
active site residues required for phosphoesterase
activity in other members of this superfamily are
intact. The archeal replicative DNA polymerases are
thought to possess intrinsic phosphatase activity that
hydrolyzes the pyrophosphate released during nucleotide
polymerization. This domain belongs to the
metallophosphatase (MPP) superfamily. MPPs are
functionally diverse, but all share a conserved domain
with an active site consisting of two metal ions
(usually manganese, iron, or zinc) coordinated with
octahedral geometry by a cage of histidine, aspartate,
and asparagine residues. The MPP superfamily includes:
Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat
debranching enzymes, YfcE-like phosphodiesterases,
purple acid phosphatases (PAPs), YbbF-like
UDP-2,3-diacylglucosamine hydrolases, and acid
sphingomyelinases (ASMases). The conserved domain is a
double beta-sheet sandwich with a di-metal active site
made up of residues located at the C-terminal side of
the sheets. This domain is thought to allow for
productive metal coordination.
Length = 243
Score = 25.7 bits (57), Expect = 4.0
Identities = 8/25 (32%), Positives = 12/25 (48%)
Query: 46 DILISGHTHKFEAYEHENKFYINPG 70
DIL +GH H + + +N G
Sbjct: 193 DILHTGHVHVYGVGVYRGVLLVNSG 217
>gnl|CDD|235208 PRK04036, PRK04036, DNA polymerase II small subunit; Validated.
Length = 504
Score = 25.3 bits (56), Expect = 4.7
Identities = 8/25 (32%), Positives = 11/25 (44%)
Query: 46 DILISGHTHKFEAYEHENKFYINPG 70
DI +GH H ++ IN G
Sbjct: 442 DIFHTGHVHINGYGKYRGVLLINSG 466
>gnl|CDD|130624 TIGR01561, gde_arch, glycogen debranching enzyme, archaeal type,
putative. The seed for this model is composed of two
uncharacterized archaeal proteins from Methanosarcina
acetivorans and Sulfolobus solfataricus. Trusted cutoff
is set so that essentially only archaeal members hit
the model. The notable exceptions to archaeal
membership are the Gram positive Clostridium
perfringens which scores much better than some other
archaea and the Cyanobacterium Nostoc sp. which scores
just above the trusted cutoff. Noise cutoff is set to
exclude the characterized eukaryotic glycogen
debranching enzyme in S. cerevisiae. These cutoffs
leave the prokaryotes Porphyromonas gingivalis and
Deinococcus radiodurans below trusted but above noise.
Multiple alignments including these last two species
exhibit sequence divergence which may suggest a subtly
different function for these prokaryotic proteins
[Energy metabolism, Biosynthesis and degradation of
polysaccharides].
Length = 575
Score = 25.4 bits (55), Expect = 4.8
Identities = 11/44 (25%), Positives = 20/44 (45%)
Query: 23 HGHDIIPWGDPEALALLQRQLDVDILISGHTHKFEAYEHENKFY 66
HG I + L+ + D +ILI G T+K +++ +
Sbjct: 25 HGLLIAALENFHGRFLILSKFDDEILIDGDTYKLATHKYPDNIS 68
>gnl|CDD|235433 PRK05368, PRK05368, homoserine O-succinyltransferase;
Provisional.
Length = 302
Score = 25.1 bits (56), Expect = 5.0
Identities = 10/27 (37%), Positives = 13/27 (48%), Gaps = 1/27 (3%)
Query: 41 RQLDVDIL-ISGHTHKFEAYEHENKFY 66
Q+D+ +L I H K EH FY
Sbjct: 63 LQVDIHLLRIDSHESKNTPAEHLENFY 89
>gnl|CDD|238193 cd00316, Oxidoreductase_nitrogenase, The nitrogenase enzyme system
catalyzes the ATP-dependent reduction of dinitrogen to
ammonia. This group contains both alpha and beta
subunits of component 1 of the three known genetically
distinct types of nitrogenase systems: a
molybdenum-dependent nitrogenase (Mo-nitrogenase), a
vanadium-dependent nitrogenase (V-nitrogenase), and an
iron-only nitrogenase (Fe-nitrogenase) and, both
subunits of Protochlorophyllide (Pchlide) reductase and
chlorophyllide (chlide) reductase. The nitrogenase
systems consist of component 1 (MoFe protein, VFe
protein or, FeFe protein respectively) and, component 2
(Fe protein). The most widespread and best characterized
nitrogenase is the Mo-nitrogenase. MoFe is an
alpha2beta2 tetramer, the alternative nitrogenases are
alpha2beta2delta2 hexamers whose alpha and beta subunits
are similar to the alpha and beta subunits of MoFe. For
MoFe, each alphabeta pair contains one P-cluster (at the
alphabeta interface) and, one molecule of iron
molybdenum cofactor (FeMoco) contained within the alpha
subunit. The Fe protein contains a single [4Fe-4S]
cluster from which, electrons are transferred to the
P-cluster of the MoFe and in turn, to FeMoCo at the site
of substrate reduction. The V-nitrogenase requires an
iron-vanadium cofactor (FeVco), the iron
only-nitrogenase an iron only cofactor (FeFeco). These
cofactors are analogous to the FeMoco. The V-nitrogenase
has P clusters identical to those of MoFe. Pchlide
reductase and chlide reductase participate in the
Mg-branch of the tetrapyrrole biosynthetic pathway.
Pchlide reductase catalyzes the reduction of the D-ring
of Pchlide during the synthesis of chlorophylls (Chl)
and bacteriochlorophylls (BChl). Chlide-a reductase
catalyzes the reduction of the B-ring of Chlide-a during
the synthesis of BChl-a. The Pchlide reductase NB
complex is a an N2B2 heterotetramer resembling
nitrogenase FeMo, N and B proteins are homologous to the
FeMo alpha and beta subunits respectively. The NB
complex may serve as a catalytic site for Pchlide
reduction and, the ZY complex as a site of chlide
reduction, similar to MoFe for nitrogen reduction.
Length = 399
Score = 25.3 bits (56), Expect = 5.2
Identities = 11/33 (33%), Positives = 19/33 (57%)
Query: 24 GHDIIPWGDPEALALLQRQLDVDILISGHTHKF 56
G +++ GD E L L R+L D++I G ++
Sbjct: 328 GTEVVDDGDLEELEELIRELKPDLIIGGSKGRY 360
>gnl|CDD|163615 cd00839, MPP_PAPs, purple acid phosphatases of the
metallophosphatase superfamily, metallophosphatase
domain. Purple acid phosphatases (PAPs) belong to a
diverse family of binuclear metallohydrolases that have
been identified and characterized in plants, animals,
and fungi. PAPs contain a binuclear metal center and
their characteristic pink or purple color derives from a
charge-transfer transition between a tyrosine residue
and a chromophoric ferric ion within the binuclear
center. PAPs catalyze the hydrolysis of a wide range of
activated phosphoric acid mono- and di-esters and
anhydrides. PAPs are distinguished from the other
phosphatases by their insensitivity to L-(+) tartrate
inhibition and are therefore also known as tartrate
resistant acid phosphatases (TRAPs). While only a few
copies of PAP-like genes are present in mammalian and
fungal genomes, multiple copies are present in plant
genomes. PAPs belong to the metallophosphatase (MPP)
superfamily. MPPs are functionally diverse, but all
share a conserved domain with an active site consisting
of two metal ions (usually manganese, iron, or zinc)
coordinated with octahedral geometry by a cage of
histidine, aspartate, and asparagine residues. The MPP
superfamily includes: Mre11/SbcD-like exonucleases,
Dbr1-like RNA lariat debranching enzymes, YfcE-like
phosphodiesterases, purple acid phosphatases (PAPs),
YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid
sphingomyelinases (ASMases). The conserved domain is a
double beta-sheet sandwich with a di-metal active site
made up of residues located at the C-terminal side of
the sheets. This domain is thought to allow for
productive metal coordination.
Length = 294
Score = 25.3 bits (56), Expect = 5.4
Identities = 7/13 (53%), Positives = 11/13 (84%)
Query: 45 VDILISGHTHKFE 57
VD+++SGH H +E
Sbjct: 194 VDLVLSGHVHAYE 206
>gnl|CDD|163620 cd00845, MPP_UshA_N_like, Escherichia coli UshA-like family,
N-terminal metallophosphatase domain. This family
includes the bacterial enzyme UshA, and related enzymes
including SoxB, CpdB, YhcR, and CD73. All members have
a similar domain architecture which includes an
N-terminal metallophosphatase domain and a C-terminal
nucleotidase domain. The N-terminal metallophosphatase
domain belongs to a large superfamily of distantly
related metallophosphatases (MPPs) that includes:
Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat
debranching enzymes, YfcE-like phosphodiesterases,
purple acid phosphatases (PAPs), YbbF-like
UDP-2,3-diacylglucosamine hydrolases, and acid
sphingomyelinases (ASMases). MPPs are functionally
diverse, but all share a conserved domain with an active
site consisting of two metal ions (usually manganese,
iron, or zinc) coordinated with octahedral geometry by a
cage of histidine, aspartate, and asparagine residues.
The conserved domain is a double beta-sheet sandwich
with a di-metal active site made up of residues located
at the C-terminal side of the sheets. This domain is
thought to allow for productive metal coordination.
Length = 252
Score = 25.3 bits (56), Expect = 5.5
Identities = 7/26 (26%), Positives = 13/26 (50%)
Query: 31 GDPEALALLQRQLDVDILISGHTHKF 56
G + L + +D+++ GHTH
Sbjct: 181 GLDDDEELAEEVPGIDVILGGHTHHL 206
>gnl|CDD|236522 PRK09450, cyaA, adenylate cyclase; Provisional.
Length = 830
Score = 24.9 bits (55), Expect = 6.6
Identities = 13/37 (35%), Positives = 17/37 (45%), Gaps = 9/37 (24%)
Query: 13 TVGQ-----FRIGLCHGHDIIPWGDPEALALLQRQLD 44
++GQ I +CH PW D E LLQR+
Sbjct: 106 SIGQSESSDLDIWVCHR----PWLDAEERQLLQRKCS 138
>gnl|CDD|143356 cd07851, STKc_p38, Catalytic domain of the Serine/Threonine Kinase,
p38 Mitogen-Activated Protein Kinase. Serine/Threonine
Kinases (STKs), p38 subfamily, catalytic (c) domain.
STKs catalyze the transfer of the gamma-phosphoryl group
from ATP to serine/threonine residues on protein
substrates. The p38 subfamily is part of a larger
superfamily that includes the catalytic domains of other
protein STKs, protein tyrosine kinases, RIO kinases,
aminoglycoside phosphotransferase, choline kinase, and
phosphoinositide 3-kinase. p38 kinases are
mitogen-activated protein kinases (MAPKs), serving as
important mediators of cellular responses to
extracellular signals. They function in the regulation
of the cell cycle, cell development, cell
differentiation, senescence, tumorigenesis, apoptosis,
pain development and pain progression, and immune
responses. p38 kinases are activated by the MAPK kinases
MKK3 and MKK6, which in turn are activated by upstream
MAPK kinase kinases including TAK1, ASK1, and MLK3, in
response to cellular stresses or inflammatory cytokines.
p38 substrates include other protein kinases and factors
that regulate transcription, nuclear export, mRNA
stability and translation. p38 kinases are drug targets
for the inflammatory diseases psoriasis, rheumatoid
arthritis, and chronic pulmonary disease. Vertebrates
contain four isoforms of p38, named alpha, beta, gamma,
and delta, which show varying substrate specificity and
expression patterns. p38alpha and p38beta are
ubiquitously expressed, p38gamma is predominantly found
in skeletal muscle, and p38delta is found in the heart,
lung, testis, pancreas, and small intestine.
Length = 343
Score = 24.9 bits (55), Expect = 6.6
Identities = 6/22 (27%), Positives = 13/22 (59%)
Query: 25 HDIIPWGDPEALALLQRQLDVD 46
++ +P A+ LL++ L +D
Sbjct: 264 KEVFSGANPLAIDLLEKMLVLD 285
>gnl|CDD|99856 cd06102, citrate_synt_like_2, Citrate synthase (CS) catalyzes the
condensation of acetyl coenzyme A (AcCoA) and
oxalacetate (OAA) to form citrate and coenzyme A (CoA),
the first step in the oxidative citric acid cycle (TCA
or Krebs cycle). Peroxisomal CS is involved in the
glyoxylate cycle. This group also includes CS proteins
which functions as a 2-methylcitrate synthase (2MCS).
2MCS catalyzes the condensation of propionyl-CoA (PrCoA)
and OAA to form 2-methylcitrate and CoA during
propionate metabolism. This group contains proteins
which functions exclusively as either a CS or a 2MCS, as
well as those with relaxed specificity which have dual
functions as both a CS and a 2MCS. The overall CS
reaction is thought to proceed through three partial
reactions and involves both closed and open
conformational forms of the enzyme: a) the carbanion or
equivalent is generated from AcCoA by base abstraction
of a proton, b) the nucleophilic attack of this
carbanion on OAA to generate citryl-CoA, and c) the
hydrolysis of citryl-CoA to produce citrate and CoA.
There are two types of CSs: type I CS and type II CSs.
Type I CSs are found in eukarya, gram-positive bacteria,
archaea, and in some gram-negative bacteria and are
homodimers with both subunits participating in the
active site. Type II CSs are unique to gram-negative
bacteria and are homohexamers of identical subunits
(approximated as a trimer of dimers). Some type II CSs
are strongly and specifically inhibited by NADH through
an allosteric mechanism. This subgroup includes both
gram-positive and gram-negative bacteria.
Length = 282
Score = 24.9 bits (55), Expect = 7.1
Identities = 10/16 (62%), Positives = 11/16 (68%)
Query: 24 GHDIIPWGDPEALALL 39
GH + P GDP A ALL
Sbjct: 184 GHPLYPDGDPRAAALL 199
>gnl|CDD|163672 cd08165, MPP_MPPE1, human MPPE1 and related proteins,
metallophosphatase domain. MPPE1 is a functionally
uncharacterized metallophosphatase domain-containing
protein. The MPPE1 gene is located on chromosome 18 and
is a candidate susceptibility gene for Bipolar disorder.
MPPE1 belongs to the metallophosphatase (MPP)
superfamily. MPPs are functionally diverse, but all
share a conserved domain with an active site consisting
of two metal ions (usually manganese, iron, or zinc)
coordinated with octahedral geometry by a cage of
histidine, aspartate, and asparagine residues. The MPP
superfamily includes: Mre11/SbcD-like exonucleases,
Dbr1-like RNA lariat debranching enzymes, YfcE-like
phosphodiesterases, purple acid phosphatases (PAPs),
YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid
sphingomyelinases (ASMases). The conserved domain is a
double beta-sheet sandwich with a di-metal active site
made up of residues located at the C-terminal side of
the sheets. This domain is thought to allow for
productive metal coordination.
Length = 156
Score = 24.6 bits (54), Expect = 7.1
Identities = 7/20 (35%), Positives = 11/20 (55%)
Query: 47 ILISGHTHKFEAYEHENKFY 66
+++SGHTH F H +
Sbjct: 125 LVLSGHTHSFCEVTHPDGTP 144
>gnl|CDD|218827 pfam05960, DUF885, Bacterial protein of unknown function
(DUF885). This family consists of several hypothetical
bacterial proteins several of which are putative
membrane proteins.
Length = 539
Score = 25.0 bits (55), Expect = 7.5
Identities = 12/50 (24%), Positives = 18/50 (36%), Gaps = 1/50 (2%)
Query: 32 DPEALALLQRQLDVDILISGHTHKFEAYEHENKFYINPGSATGAFNPLEP 81
DP L+ R +D DIL + E +Y P + + P
Sbjct: 43 DPAGLSPEDR-VDYDILRYELENLLALEELRYWYYRYPLNQLSGAHSGLP 91
>gnl|CDD|217821 pfam03969, AFG1_ATPase, AFG1-like ATPase. This family of proteins
contains a P-loop motif and are predicted to be ATPases.
Length = 361
Score = 24.7 bits (54), Expect = 7.8
Identities = 11/53 (20%), Positives = 18/53 (33%), Gaps = 5/53 (9%)
Query: 36 LALLQRQLDVDILISGHTHKFEAYEHENKFYINPGSATGAFNPLEPLNGRYAN 88
+ L + H H+F H+ + G +PL R+AN
Sbjct: 78 MDSFFESLPGERKRRTHFHRFMFRVHDELTTLQGGD-----DPLPIAADRFAN 125
>gnl|CDD|193540 cd05664, M20_Acy1_like6, M20 Peptidase Aminoacylase 1 subfamily.
Peptidase M20 family, Uncharacterized subfamily of
proteins predicted as putative amidohydrolases or
hippurate hydrolases. These are a class of zinc binding
homodimeric enzymes involved in the hydrolysis of
N-acetylated proteins. N-terminal acetylation of
proteins is a widespread and highly conserved process
that is involved in the protection and stability of
proteins. Several types of aminoacylases can be
distinguished on the basis of substrate specificity.
Aminoacylase 1 (ACY1) breaks down cytosolic aliphatic
N-acyl-alpha-amino acids (except L-aspartate),
especially N-acetyl-methionine and acetyl-glutamate into
L-amino acids and an acyl group. However, ACY1 can also
catalyze the reverse reaction, the synthesis of
acetylated amino acids. ACY1 may also play a role in
xenobiotic bioactivation as well as in the inter-organ
processing of amino acid-conjugated xenobiotic
derivatives (S-substituted-N-acetyl-L-cysteine).
Length = 398
Score = 24.8 bits (55), Expect = 7.8
Identities = 9/19 (47%), Positives = 10/19 (52%), Gaps = 2/19 (10%)
Query: 11 VVTVGQFRIGLCHGHDIIP 29
VVTVG G +IIP
Sbjct: 230 VVTVGSLHAG--TKANIIP 246
>gnl|CDD|235407 PRK05322, PRK05322, galactokinase; Provisional.
Length = 387
Score = 24.8 bits (55), Expect = 8.8
Identities = 9/28 (32%), Positives = 16/28 (57%)
Query: 34 EALALLQRQLDVDILISGHTHKFEAYEH 61
+AL LQ++LD+ L +F+ Y +
Sbjct: 233 KALEELQKKLDIKSLGELTEEEFDEYSY 260
>gnl|CDD|220064 pfam08901, DUF1847, Protein of unknown function (DUF1847). This
family of proteins are functionally uncharacterized.
THey contain 4 N-terminal cysteines that may form a zinc
binding domain.
Length = 157
Score = 24.5 bits (54), Expect = 8.9
Identities = 6/10 (60%), Positives = 8/10 (80%)
Query: 19 IGLCHGHDII 28
+GLC GHD +
Sbjct: 136 VGLCVGHDSL 145
>gnl|CDD|137627 PRK09982, PRK09982, universal stress protein UspD; Provisional.
Length = 142
Score = 24.6 bits (53), Expect = 9.0
Identities = 9/24 (37%), Positives = 14/24 (58%)
Query: 33 PEALALLQRQLDVDILISGHTHKF 56
PE L + ++ D+L+ GH H F
Sbjct: 92 PETLLEIMQKEQCDLLVCGHHHSF 115
>gnl|CDD|237435 PRK13579, gcvT, glycine cleavage system aminomethyltransferase T;
Provisional.
Length = 370
Score = 24.5 bits (54), Expect = 9.8
Identities = 10/20 (50%), Positives = 11/20 (55%), Gaps = 1/20 (5%)
Query: 20 GLC-HGHDIIPWGDPEALAL 38
GLC +GHDI P AL
Sbjct: 237 GLCLYGHDIDTTTTPVEAAL 256
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
0.318 0.139 0.432
Gapped
Lambda K H
0.267 0.0767 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,812,820
Number of extensions: 398992
Number of successful extensions: 487
Number of sequences better than 10.0: 1
Number of HSP's gapped: 483
Number of HSP's successfully gapped: 68
Length of query: 91
Length of database: 10,937,602
Length adjustment: 58
Effective length of query: 33
Effective length of database: 8,365,070
Effective search space: 276047310
Effective search space used: 276047310
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: 53 (24.1 bits)