RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy149
(86 letters)
>gnl|CDD|227539 COG5214, POL12, DNA polymerase alpha-primase complex,
polymerase-associated subunit B [DNA replication,
recombination, and repair].
Length = 581
Score = 55.0 bits (132), Expect = 2e-10
Identities = 26/86 (30%), Positives = 39/86 (45%), Gaps = 4/86 (4%)
Query: 3 LTRRSLSMFVSAGPYTQSDTLSYKPLEDLIALTVQQEPDVLILIGPLLDTSHPLLLNGSL 62
+ S+ +GPY D LS PL D I + DVLILIGP +D +H L+ G+
Sbjct: 300 TNNQPTSIVAFSGPYGPRDDLSGSPLFDAIDRVNANDVDVLILIGPFIDINHILIQYGAT 359
Query: 63 ----AETFEDFYVKLIDSIVQPLEKP 84
++ ++ I I+ P
Sbjct: 360 QSTPDSMLKELFIPRITPILDRNAGP 385
>gnl|CDD|217857 pfam04042, DNA_pol_E_B, DNA polymerase alpha/epsilon subunit B.
This family contains a number of DNA polymerase
subunits. The B subunit of the DNA polymerase alpha
plays an essential role at the initial stage of DNA
replication in S. cerevisiae and is phosphorylated in a
cell cycle-dependent manner. DNA polymerase epsilon is
essential for cell viability and chromosomal DNA
replication in budding yeast. In addition, DNA
polymerase epsilon may be involved in DNA repair and
cell-cycle checkpoint control. The enzyme consists of
at least four subunits in mammalian cells as well as in
yeast. The largest subunit of DNA polymerase epsilon is
responsible for polymerase epsilon is responsible for
polymerase activity. In mouse, the DNA polymerase
epsilon subunit B is the second largest subunit of the
DNA polymerase. A part of the N-terminal was found to
be responsible for the interaction with SAP18.
Experimental evidence suggests that this subunit may
recruit histone deacetylase to the replication fork to
modify the chromatin structure.
Length = 189
Score = 40.4 bits (95), Expect = 2e-05
Identities = 18/52 (34%), Positives = 28/52 (53%)
Query: 27 PLEDLIALTVQQEPDVLILIGPLLDTSHPLLLNGSLAETFEDFYVKLIDSIV 78
L DL+ PD LIL GP L H L+ + + T++ ++KL+D I+
Sbjct: 2 LLRDLLDGYNAAPPDRLILAGPFLSAPHNLIASSKVNLTYDFLFLKLLDGIL 53
>gnl|CDD|236899 PRK11340, PRK11340, phosphodiesterase YaeI; Provisional.
Length = 271
Score = 28.7 bits (64), Expect = 0.29
Identities = 11/29 (37%), Positives = 19/29 (65%)
Query: 28 LEDLIALTVQQEPDVLILIGPLLDTSHPL 56
+ D IAL ++Q+PD+++L G + PL
Sbjct: 69 ISDAIALGIEQKPDLILLGGDYVLFDMPL 97
>gnl|CDD|203836 pfam07997, DUF1694, Protein of unknown function (DUF1694). This
family contains many hypothetical proteins.
Length = 120
Score = 28.3 bits (64), Expect = 0.29
Identities = 17/48 (35%), Positives = 26/48 (54%), Gaps = 6/48 (12%)
Query: 31 LIALTVQQ--EPDVLILIGPLLDTSHP---LLLNGSLAETFEDFYVKL 73
++ALT++Q +P V L +P LLLNG+L + Y+KL
Sbjct: 37 VLALTIKQVLDPKVYKEFEQEL-KDYPNYTLLLNGNLDYDIQSQYIKL 83
>gnl|CDD|239114 cd02648, nuc_hydro_1, NH_1: A subgroup of nucleoside hydrolases.
This group contains fungal proteins similar to
nucleoside hydrolases. Nucleoside hydrolases cleave the
N-glycosidic bond in nucleosides generating ribose and
the respective base. These enzymes vary in their
substrate specificity. .
Length = 367
Score = 27.5 bits (61), Expect = 0.82
Identities = 14/44 (31%), Positives = 23/44 (52%), Gaps = 7/44 (15%)
Query: 16 PYTQSDTLSYKPLEDLIALTVQQEPD--VLIL-IGPLLDTSHPL 56
P T SD +Y + D++ ++EPD V I +GPL + +
Sbjct: 129 PLTPSDKPAYDVILDIL----REEPDHTVTIAALGPLTNLAAAA 168
>gnl|CDD|117685 pfam09129, Chol_subst-bind, Cholesterol oxidase, substrate-binding.
The substrate-binding domain found in Cholesterol
oxidase is composed of an eight-stranded mixed
beta-pleated sheet and six alpha-helices. This domain is
positioned over the isoalloxazine ring system of the FAD
cofactor bound by FAD_binding_4 (PF:PF01565) and forms
the roof of the active site cavity, allowing for
catalysis of oxidation and isomerisation of cholesterol
to cholest-4-en-3-one.
Length = 321
Score = 26.8 bits (59), Expect = 1.2
Identities = 15/64 (23%), Positives = 22/64 (34%), Gaps = 7/64 (10%)
Query: 5 RRSLSMFVSAGPYTQ--SDTLSYKPLEDLIALTVQQEPDVLILIGPLLDTSHPLLLNGSL 62
+ +GPY SD + +P+ DLI P + L G + L
Sbjct: 57 TKPDGAREVSGPYNYPFSDNIP-EPISDLIGAINAGNPGLAPLFGKAQYE----ITKLGL 111
Query: 63 AETF 66
A T
Sbjct: 112 AATN 115
>gnl|CDD|226315 COG3792, COG3792, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 122
Score = 26.2 bits (58), Expect = 1.5
Identities = 11/36 (30%), Positives = 15/36 (41%), Gaps = 7/36 (19%)
Query: 41 DVLILIGPLLDTSHPLL-------LNGSLAETFEDF 69
D L+G LLD L + G++ E E F
Sbjct: 48 DFFFLLGDLLDEGKLKLGNRKGQFIEGTIEELVEMF 83
>gnl|CDD|163626 cd07383, MPP_Dcr2, Saccharomyces cerevisiae DCR2 phosphatase and
related proteins, metallophosphatase domain. DCR2
phosphatase (Dosage-dependent Cell Cycle Regulator 2)
functions together with DCR1 (Gid8) in a common pathway
to accelerate initiation of DNA replication in
Saccharomyces cerevisiae. Genetic analysis suggests
that DCR1 functions upstream of DCR2. DCR2 interacts
with and dephosphorylates Sic1, an inhibitor of mitotic
cyclin/cyclin-dependent kinase complexes, which may
serve to trigger the initiation of cell division. DCR2
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 = 199
Score = 26.5 bits (59), Expect = 1.5
Identities = 13/51 (25%), Positives = 19/51 (37%), Gaps = 4/51 (7%)
Query: 37 QQEPDVLILIGPLLDTSHPLL--LNGSL--AETFEDFYVKLIDSIVQPLEK 83
+ + + I +LD P L L G L E D +D V P+
Sbjct: 24 EADLKTVAFIERVLDAEKPDLVVLTGDLITGENTNDNSTSALDKAVSPMID 74
>gnl|CDD|223318 COG0240, GpsA, Glycerol-3-phosphate dehydrogenase [Energy
production and conversion].
Length = 329
Score = 26.4 bits (59), Expect = 1.7
Identities = 12/49 (24%), Positives = 23/49 (46%), Gaps = 3/49 (6%)
Query: 31 LIALTVQQEPDVLILIGPLLDTSHPLLLNGSLAETFEDFYVKLIDSIVQ 79
+IA+ Q +VL + PLL ++ S + E +L+ I++
Sbjct: 76 VIAVPSQALREVLRQLKPLLLKDAIIV---SATKGLEPETGRLLSEIIE 121
>gnl|CDD|181869 PRK09453, PRK09453, phosphodiesterase; Provisional.
Length = 182
Score = 26.4 bits (59), Expect = 1.9
Identities = 11/32 (34%), Positives = 15/32 (46%), Gaps = 1/32 (3%)
Query: 20 SDTL-SYKPLEDLIALTVQQEPDVLILIGPLL 50
SDT S E + L Q D L+ +G +L
Sbjct: 7 SDTHGSLPATEKALELFAQSGADWLVHLGDVL 38
>gnl|CDD|183801 PRK12864, PRK12864, YciI-like protein; Reviewed.
Length = 89
Score = 24.9 bits (55), Expect = 3.2
Identities = 8/26 (30%), Positives = 13/26 (50%)
Query: 29 EDLIALTVQQEPDVLILIGPLLDTSH 54
L L +E +LI +GP D ++
Sbjct: 24 AHLDRLAKLKEQGILITLGPTKDLTY 49
>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 = 25.4 bits (56), Expect = 3.4
Identities = 7/32 (21%), Positives = 22/32 (68%)
Query: 24 SYKPLEDLIALTVQQEPDVLILIGPLLDTSHP 55
++ E+++ L ++++ D +++ G L D+++P
Sbjct: 26 QFEAFEEIVELAIEEKVDFVLIAGDLFDSNNP 57
>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 = 25.3 bits (56), Expect = 4.1
Identities = 10/28 (35%), Positives = 16/28 (57%)
Query: 28 LEDLIALTVQQEPDVLILIGPLLDTSHP 55
LE L+ +PD+++L G L+D S
Sbjct: 21 LERLVEKINALKPDLVVLTGDLVDGSVD 48
>gnl|CDD|179637 PRK03719, PRK03719, ecotin; Provisional.
Length = 166
Score = 24.6 bits (54), Expect = 6.3
Identities = 29/105 (27%), Positives = 43/105 (40%), Gaps = 29/105 (27%)
Query: 1 MTLTRRSLSMFVSAGPYTQSDTLSYKPLED--------------LIALTVQQ-EPD--VL 43
L+ F +A + + + SY+PLE +I L Q+ E D V
Sbjct: 7 TIAPAVLLAAFAAASAWAPAASSSYQPLEKIKPYPQAEKGMKRQVITLPPQEDESDYKVE 66
Query: 44 ILIGPLLDTS---HPLLLNGSL-AETFE----DFYVKLIDSIVQP 80
+LIG L+ H L G L +T E D+YV +D + P
Sbjct: 67 LLIGQTLEVDCNQH--RLGGELEEKTLEGWGYDYYV--VDKVSGP 107
>gnl|CDD|216395 pfam01261, AP_endonuc_2, Xylose isomerase-like TIM barrel. This
TIM alpha/beta barrel structure is found in xylose
isomerase and in endonuclease IV (EC:3.1.21.2). This
domain is also found in the N termini of bacterial
myo-inositol catabolism proteins. These are involved in
the myo-inositol catabolism pathway, and is required for
growth on myo-inositol in Rhizobium leguminosarum bv.
viciae.
Length = 202
Score = 24.7 bits (54), Expect = 6.6
Identities = 9/46 (19%), Positives = 12/46 (26%), Gaps = 5/46 (10%)
Query: 46 IGPLLDTSHPLLLNGSLAETFEDF--YVKLI---DSIVQPLEKPGH 86
+G LDT H G E + + D H
Sbjct: 149 VGLCLDTGHAFAAGGDPEELLRRLGDRIGHVHLKDVKGLGAGVDRH 194
>gnl|CDD|220774 pfam10477, EIF4E-T, Nucleocytoplasmic shuttling protein for mRNA
cap-binding EIF4E. EIF4E-T is the transporter protein
for shuttling the mRNA cap-binding protein EIF4E
protein, targeting it for nuclear import. EIF4E-T
contains several key binding domains including two
functional leucine-rich NESs (nuclear export signals)
between residues 438-447 and 613-638 in the human
protein. The other two binding domains are an
EIF4E-binding site, between residues 27-42 in Q9EST3,
and a bipartite NLS (nuclear localisation signals)
between 194-211, and these lie in family EIF4E-T_N.
EIF4E is the eukaryotic translation initiation factor 4E
that is the rate-limiting factor for cap-dependent
translation initiation.
Length = 520
Score = 24.9 bits (53), Expect = 6.6
Identities = 8/22 (36%), Positives = 13/22 (59%)
Query: 11 FVSAGPYTQSDTLSYKPLEDLI 32
+ SAGP +Q +T+ +D I
Sbjct: 205 WFSAGPTSQLETIELIGFDDKI 226
>gnl|CDD|163631 cd07388, MPP_Tt1561, Thermus thermophilus Tt1561 and related
proteins, metallophosphatase domain. This family
includes bacterial proteins related to Tt1561 (also
known as Aq1956 in Aquifex aeolicus), an
uncharacterized Thermus thermophilus protein. The
conserved 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, and is thought to allow for productive
metal coordination. However, the active site residues
required for phosphoesterase activity in other members
of this superfamily are poorly conserved in this
functionally uncharacterized family.
Length = 224
Score = 24.8 bits (54), Expect = 6.7
Identities = 15/58 (25%), Positives = 26/58 (44%), Gaps = 7/58 (12%)
Query: 28 LEDLIALTVQQEPDVLILIGPLLDTSHPLLLNGSLAETFEDFYVKLIDSIVQPLEKPG 85
LE L+ L + D ++LIG LL + +E + F+ L ++ + PG
Sbjct: 20 LEKLVGLAPETGADAIVLIGNLLP-------KAAKSEDYAAFFRILGEAHLPTFYVPG 70
>gnl|CDD|236848 PRK11107, PRK11107, hybrid sensory histidine kinase BarA;
Provisional.
Length = 919
Score = 24.8 bits (55), Expect = 6.9
Identities = 11/47 (23%), Positives = 25/47 (53%), Gaps = 1/47 (2%)
Query: 11 FVSAGPYTQSDTLSY-KPLEDLIALTVQQEPDVLILIGPLLDTSHPL 56
FV++ + +++ + L L+V+++ D LIL P++ S+
Sbjct: 96 FVTSNYHLDFESMRLPEGLPIPRLLSVERDGDSLILRTPIISESYSP 142
>gnl|CDD|227268 COG4932, COG4932, Predicted outer membrane protein [Cell envelope
biogenesis, outer membrane].
Length = 1531
Score = 24.4 bits (53), Expect = 9.8
Identities = 9/29 (31%), Positives = 14/29 (48%)
Query: 47 GPLLDTSHPLLLNGSLAETFEDFYVKLID 75
G L T+ L G+L +TF+ + D
Sbjct: 744 GNLTGTAIALNATGTLTKTFDKNVETVSD 772
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 0.137 0.386
Gapped
Lambda K H
0.267 0.0798 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,304,947
Number of extensions: 350816
Number of successful extensions: 339
Number of sequences better than 10.0: 1
Number of HSP's gapped: 339
Number of HSP's successfully gapped: 26
Length of query: 86
Length of database: 10,937,602
Length adjustment: 54
Effective length of query: 32
Effective length of database: 8,542,486
Effective search space: 273359552
Effective search space used: 273359552
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)