RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11941
(313 letters)
>gnl|CDD|233033 TIGR00583, mre11, DNA repair protein (mre11). All proteins in this
family for which functions are known are subunits of a
nuclease complex made up of multiple proteins including
MRE11 and RAD50 homologs. The functions of this nuclease
complex include recombinational repair and non-homolgous
end joining. This family is based on the phylogenomic
analysis of JA Eisen (1999, Ph.D. Thesis, Stanford
University). The proteins in this family are distantly
related to proteins in the SbcCD complex of bacteria
[DNA metabolism, DNA replication, recombination, and
repair].
Length = 402
Score = 338 bits (868), Expect = e-115
Identities = 142/298 (47%), Positives = 199/298 (66%), Gaps = 4/298 (1%)
Query: 20 NTIRIMIASDIHLGYLETDRERGNDSFVSFEEILEQALDQEVDMVLLGGDLFHINKPSPT 79
+TIRI+I++D H+GY E D RG+DS+V+F EIL+ A +Q+VDM+LLGGDLFH NKPS
Sbjct: 2 DTIRILISTDNHVGYGENDPVRGDDSWVTFNEILQIAKEQDVDMILLGGDLFHENKPSRK 61
Query: 80 TLKKCLETLRKYCIGDRSVFIDVISDPKLVMCND---HVNYMDPNLNISLPVFTINGNHD 136
+L + L +LR C+GD+ ++++SD LV + +VNY DPN+N+++PVF+I+GNHD
Sbjct: 62 SLYQVLRSLRLNCLGDKPCELELLSDASLVFGDTAFCNVNYEDPNINVAIPVFSIHGNHD 121
Query: 137 DPSGPELVAALDIVSNSGLVNYFGKCTNLNEITLNPLIIQKNETKVAIFGLGYVKDERLC 196
DPSG ALDI+ +GLVNYFG+ + I ++P+++QK TK+A++G+ V+DERL
Sbjct: 122 DPSGDGRYCALDILQATGLVNYFGRVPENDNIVVSPILLQKGFTKLALYGISNVRDERLY 181
Query: 197 NMIKHNKVKYMKPTDDKDIIY-ILVLHQNRPERGTVKNIAEDSIPSFFHFILWGHEHECR 255
+ NKVK+++P +D + +L +HQN + E IP F+ ++WGHEHEC
Sbjct: 182 RTFRDNKVKFLRPNLYRDEWFNLLTVHQNHSAHTPTSYLPESFIPDFYDLVIWGHEHECL 241
Query: 256 IKPEYNTKQRFHVCQPGSPVATSLCAGEAVQKKCGILMCNKQNYKLVPRSLETVRPFV 313
I P YN Q F V QPGS VATSL GEA K IL + + L L TVRPFV
Sbjct: 242 IDPVYNPTQGFTVLQPGSTVATSLSPGEAAPKHVFILNITGRKFHLEKIPLRTVRPFV 299
>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 = 176 bits (447), Expect = 3e-54
Identities = 76/265 (28%), Positives = 111/265 (41%), Gaps = 51/265 (19%)
Query: 23 RIMIASDIHLGYLE---TDRERGNDSFVSFEEILEQALDQEVDMVLLGGDLFHINKPSPT 79
R + +D HLG + R D F +FEEI+E A++++VD VL+ GDLF N PSP
Sbjct: 1 RFLHTADWHLGKPLKGLSRDRRREDQFEAFEEIVELAIEEKVDFVLIAGDLFDSNNPSPE 60
Query: 80 TLKKCLETLRKYCIGDRSVFIDVISDPKLVMCNDHVNYMDPNLNISLPVFTINGNHDDPS 139
L+ +E LR+ +PVF I GNHD PS
Sbjct: 61 ALELLIEALRRLKE------------------------------AGIPVFIIAGNHDSPS 90
Query: 140 GPELVAALDIVSNSGLVNYFGKCTNLNEITLNPLIIQKNETKVAIFGLGYVKDERLCNMI 199
++ L +S LV E L PL++ K T VAI+GL Y++ RL +++
Sbjct: 91 RLGALSPLLALSGLHLVGV-------EEDVLTPLLLPKGGTGVAIYGLPYLRRSRLRDLL 143
Query: 200 KHNKVKYMKPTDDKDIIYILVLHQNR-----PERGTVKNIAEDSIPSFFHFILWGHEHEC 254
+ D D IL+LH + + E +P+ F ++ GH H
Sbjct: 144 A--DAELRPRPLDPDDFNILLLHGGVAGAGPSDSERAPFVPEALLPAGFDYVALGHIHRP 201
Query: 255 RIKPEYNTKQRFHVCQPGSPVATSL 279
+I + PGSP S
Sbjct: 202 QIIL----GGGPPIVYPGSPEGLSF 222
>gnl|CDD|223497 COG0420, SbcD, DNA repair exonuclease [DNA replication,
recombination, and repair].
Length = 390
Score = 119 bits (301), Expect = 4e-31
Identities = 78/284 (27%), Positives = 120/284 (42%), Gaps = 52/284 (18%)
Query: 22 IRIMIASDIHLGYL-ETDRERGNDSFVSFEEILEQALDQEVDMVLLGGDLFHINKPSPTT 80
++I+ SD HLG R D +F+E+LE A +++VD VL+ GDLF N PSP
Sbjct: 1 MKILHTSDWHLGSKQLNLPSRLEDQKKAFDELLEIAKEEKVDFVLIAGDLFDTNNPSPRA 60
Query: 81 LKKCLETLRKYCIGDRSVFIDVISDPKLVMCNDHVNYMDPNLNISLPVFTINGNHDDPSG 140
LK LE LR+ +PV I GNHD PS
Sbjct: 61 LKLFLEALRRLKD------------------------------AGIPVVVIAGNHDSPSR 90
Query: 141 PELVAALDIVSNSGLVNYFGKCT---NLNEITLNPLIIQK-NETKVAIFGLGYVKDERLC 196
+ L +++N GL G+ EI P +I + V GL ++ E+
Sbjct: 91 LSEASPLLLLNNLGLHGVVGRLVHEIRPPEIVAAPWLIPGPDPDVVFFLGLNGLEKEQF- 149
Query: 197 NMIKHNKVKYMKPTDDKDIIYILVLHQ--NRPERGTVKNIAEDSIP------SFFHFILW 248
++ H + DD ILVLHQ + G +++A ++ F ++
Sbjct: 150 ELLLHKGLLSALDPDDDPS--ILVLHQSIDALTSGAERDLALGTVDLSLLPKGGFDYVAL 207
Query: 249 GHEHECRIKPEYNTKQRFHVCQPGSPVATSLCAGEAVQKKCGIL 292
GH H+ ++ P+ + + PGSP S GE ++K +L
Sbjct: 208 GHIHKRQVIPKEDP----PIVYPGSPERYS--FGEEGERKGVVL 245
>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 = 54.4 bits (130), Expect = 7e-09
Identities = 37/241 (15%), Positives = 58/241 (24%), Gaps = 65/241 (26%)
Query: 23 RIMIASDIHLGYLETDRERGNDSFVSFEEILEQALDQEVDMVLLGGDLFHINKPSPTTLK 82
RI++ D+H G D +LE + + D+VL GDL PS L
Sbjct: 1 RILVIGDLHGGL---------DDLDLLLLLLELLGEPKPDLVLFLGDLVDRGPPSLEVLA 51
Query: 83 KCLETLRKYCIGDRSVFIDVISDPKLVMCNDHVNYMDPNLNISLPVFTINGNHDDPSGPE 142
K PV+ + GNHD SG
Sbjct: 52 LLFALKLKAPG---------------------------------PVYLVRGNHDFDSGNS 78
Query: 143 LVAALDIVSNSGLVNYFGKCTNLNEITLNPLIIQKNETKVAIFGLGYVKDERLCNMIKHN 202
+ + V G +N + + +
Sbjct: 79 ELGFYLECAGLPYVLGNGDVSNGTVEIIGLSSLYGKGGGLVWE-------------EFLE 125
Query: 203 KVKYMKPTDDKDIIYILVLHQNRPERGTVKNIAEDSIPSFF---------HFILWGHEHE 253
+ + D IL++H + +L GH H
Sbjct: 126 LLDLLLLAALVDGK-ILLVHGPLSPSLDSGDDIYLFGEEALEDLLKDNGVDLVLRGHTHV 184
Query: 254 C 254
Sbjct: 185 P 185
>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 = 49.2 bits (118), Expect = 6e-07
Identities = 55/232 (23%), Positives = 79/232 (34%), Gaps = 70/232 (30%)
Query: 22 IRIMIASDIHLGYLETDRERGNDSFVSFEEILEQALDQEVDMVLLGGDLFHINKPSPTTL 81
+RI SD+HLG + + E ++E+ + D+V+L GDL S L
Sbjct: 2 LRIAHLSDLHLG------PFVSRERL--ERLVEKINALKPDLVVLTGDLV---DGSVDVL 50
Query: 82 KKCLETLRKYCIGDRSVFIDVISDPKLVMCNDHVNYMDPNLNISLPVFTINGNHDDPSGP 141
+ LE L+K L L V+ + GNHD SG
Sbjct: 51 ELLLELLKK-------------------------------LKAPLGVYAVLGNHDYYSGD 79
Query: 142 ELVAALDIVSNSGLVNYFGKCTNL-NEITLNPLIIQKNETKVAIFGLGYVKDERLCNMIK 200
E + S T L NE I + I G+ R
Sbjct: 80 EENWIEALESAG--------ITVLRNESVE----ISVGGATIGIAGVDDGLGRR------ 121
Query: 201 HNKVKYMKPTDDKDIIYILVLHQNRPERGTVKNIAEDSIPSFFHFILWGHEH 252
+ K +K D+ D IL+ HQ P+ AE++ L GH H
Sbjct: 122 PDLEKALKGLDEDDPN-ILLAHQ--PD------TAEEAAAWGVDLQLSGHTH 164
>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 = 42.6 bits (101), Expect = 9e-05
Identities = 30/125 (24%), Positives = 41/125 (32%), Gaps = 45/125 (36%)
Query: 28 SDIHLGYLETDRERGNDSFVSFEEILEQ--ALDQEVDMVLLGGDLFHINKPSP---TTLK 82
SD+HL G D+ S E +L AL D+VL+ GDL SP L+
Sbjct: 6 SDLHLRADGEGALLGVDTAASLEAVLAHINALHPRPDLVLVTGDLTD--DGSPESYERLR 63
Query: 83 KCLETLRKYCIGDRSVFIDVISDPKLVMCNDHVNYMDPNLNISLPVFTINGNHDDPSGPE 142
+ L L +PV+ + GNHDD
Sbjct: 64 ELLAALP------------------------------------IPVYLLPGNHDDR--AA 85
Query: 143 LVAAL 147
+ A
Sbjct: 86 MRAVF 90
>gnl|CDD|233056 TIGR00619, sbcd, exonuclease SbcD. All proteins in this family for
which functions are known are double-stranded DNA
exonuclease (as part of a complex with SbcC homologs).
This complex functions in the initiation of
recombination and recombinational repair and is
particularly important in regulating the stability of
DNA sections that can form secondary structures. This
family is likely homologous to the MRE11 family. This
family is based on the phylogenomic analysis of JA Eisen
(1999, Ph.D. Thesis, Stanford University) [DNA
metabolism, DNA replication, recombination, and repair].
Length = 253
Score = 38.9 bits (91), Expect = 0.002
Identities = 50/284 (17%), Positives = 82/284 (28%), Gaps = 51/284 (17%)
Query: 23 RIMIASDIHLGYLETDRERGNDSFVSFEEILEQALDQEVDMVLLGGDLFHINKPSPTTLK 82
RI+ SD HLG R + +++LE A +++D +L+ GD+F P
Sbjct: 2 RILHTSDWHLGKTLEGVSRLAEQKAFLDDLLEFAKAEQIDALLVAGDVFDTANPPAEA-- 59
Query: 83 KCLETLRKYCIGDRSVFIDVISDPKLVMCNDHVNYMDPNLNISLPVFTINGNHDDPSGPE 142
+ +F + +P+ I+GNHD
Sbjct: 60 -------------QELFNAFFRNLSDANP--------------IPIVVISGNHDSAQRLS 92
Query: 143 LVAALDIVSNSGLVNYFGK-------CTNLNEITLNPLIIQKNETKVAIFGLGYVKDERL 195
L I +V + N L + + L
Sbjct: 93 AAKKLLIELGVFVVGFPVGDPQILLLKDTANGELLIVGLPLLPREALLTRAGLDGFGLEL 152
Query: 196 CNMIKHNKV----KYMKPTDDKDIIYILVLH-------QNRPERGTVKNIAEDSIPSFFH 244
+ K+ + + D D+ IL+ H ++ ER F
Sbjct: 153 LLLHLDVKLRQALEGLIRRLDPDLPKILLAHLFTAGATKSATERRIYIGFTYAVPLINFP 212
Query: 245 FILWGHEHECRIKPEYNTKQRFHVCQPGSPVATSLCAGEAVQKK 288
+ I +K R V GSP S EA + K
Sbjct: 213 EADYVALGHHHIHK--ISKGRERVRYSGSPFPLS--FDEAGEDK 252
>gnl|CDD|181869 PRK09453, PRK09453, phosphodiesterase; Provisional.
Length = 182
Score = 34.8 bits (81), Expect = 0.026
Identities = 14/51 (27%), Positives = 21/51 (41%), Gaps = 13/51 (25%)
Query: 23 RIMIASDIHLGYLETDRERGNDSFVSFEEILEQALDQEVDMVLLGGD-LFH 72
++M ASD H S + E+ LE D ++ GD L+H
Sbjct: 2 KLMFASDTH------------GSLPATEKALELFAQSGADWLVHLGDVLYH 40
>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 = 31.5 bits (71), Expect = 0.21
Identities = 22/112 (19%), Positives = 30/112 (26%), Gaps = 43/112 (38%)
Query: 25 MIASDIHLGYLETDRERGNDSFVSFEEILEQALDQEVDMVLLGGDLFHINKPSPTTLKKC 84
+ SDIH GN + A ++ D VL+ GDL L
Sbjct: 1 AVISDIH----------GNLEALEAVLEAALAAAEKPDFVLVLGDLVGDGPDPEEVLAAA 50
Query: 85 LETLRKYCIGDRSVFIDVISDPKLVMCNDHVNYMDPNLNISLPVFTINGNHD 136
L L +PV+ + GNHD
Sbjct: 51 LALLLLL---------------------------------GIPVYVVPGNHD 69
>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 = 31.9 bits (73), Expect = 0.26
Identities = 22/85 (25%), Positives = 38/85 (44%), Gaps = 12/85 (14%)
Query: 25 MIASDIHLGYLETDRERG-NDSFVSFEEILEQALDQEV-----DMVLLGGDLFHINKPSP 78
++ +D+HLG E R RG E+ LE+ LD+ + + +++ GDL H
Sbjct: 1 LVVADLHLGKEEELRRRGILLPRGQTEDTLER-LDRLIEEYGPERLIILGDLKHSFGGLS 59
Query: 79 TTLKKCLETLRKYCIGDRSVFIDVI 103
+ + LR + +DVI
Sbjct: 60 RQEFEEVAFLRL-----LAKDVDVI 79
>gnl|CDD|223808 COG0737, UshA, 5'-nucleotidase/2',3'-cyclic phosphodiesterase and
related esterases [Nucleotide transport and metabolism].
Length = 517
Score = 32.4 bits (74), Expect = 0.27
Identities = 29/178 (16%), Positives = 57/178 (32%), Gaps = 48/178 (26%)
Query: 21 TIRIMIASDIH---LGYLETDRERGNDSFVSFEEILEQALDQEVD-MVLLGGDLFHINKP 76
+ I+ +D+H Y D + +++Q + + ++L GDL +
Sbjct: 26 KLTILHTNDLHGHLEPYDYDDDGDTDGGLARIATLVKQLRAENKNVLLLDAGDLIQGSPL 85
Query: 77 SPTTLKKCLETLRKYCIGDRSVFIDVISDPKLVMCNDHVNYMDPNLNISLPVFTINGNHD 136
S + +D+ +N + + T+ GNH+
Sbjct: 86 S-------------DYLTKGEPTVDL------------LNALGYD------AMTL-GNHE 113
Query: 137 DPSGPELV------AALDIVSNSGLVNYFGKCTNLNEITLNPLIIQ-KNETKVAIFGL 187
G E + A ++S N + K + P I+ K+ I GL
Sbjct: 114 FDYGLEALARLLDEAKFPVLS----ANVYDKNSTGPPF-FKPYAIKEVGGVKIGIIGL 166
>gnl|CDD|219044 pfam06470, SMC_hinge, SMC proteins Flexible Hinge Domain. This
family represents the hinge region of the SMC
(Structural Maintenance of Chromosomes) family of
proteins. The hinge region is responsible for formation
of the DNA interacting dimer. It is also possible that
the precise structure of it is an essential determinant
of the specificity of the DNA-protein interaction.
Length = 117
Score = 30.7 bits (70), Expect = 0.29
Identities = 19/66 (28%), Positives = 29/66 (43%), Gaps = 8/66 (12%)
Query: 45 SFVSFEEILEQALDQEVDMVLLGGDLFHINKPSPTTLKKCLETLRKYCIGDRSVFI--DV 102
+ +E E+A++ LGG L I T K +E L+K +G R+ F+ D
Sbjct: 10 DLIEVDEGYEKAVE-----AALGGRLQAIVVDDEETAKAAIEFLKKNNLG-RATFLPLDR 63
Query: 103 ISDPKL 108
I L
Sbjct: 64 IKPRPL 69
>gnl|CDD|182871 PRK10966, PRK10966, exonuclease subunit SbcD; Provisional.
Length = 407
Score = 32.2 bits (74), Expect = 0.31
Identities = 17/52 (32%), Positives = 31/52 (59%), Gaps = 4/52 (7%)
Query: 22 IRIMIASDIHLG--YLETDRERGNDSFVSFEEILEQALDQEVDMVLLGGDLF 71
+RI+ SD HLG + R + +F+ + +LEQ + +VD +++ GD+F
Sbjct: 1 MRILHTSDWHLGQNFYSKSRAAEHQAFLDW--LLEQVQEHQVDAIIVAGDIF 50
>gnl|CDD|236899 PRK11340, PRK11340, phosphodiesterase YaeI; Provisional.
Length = 271
Score = 31.7 bits (72), Expect = 0.41
Identities = 30/124 (24%), Positives = 44/124 (35%), Gaps = 47/124 (37%)
Query: 22 IRIMIASDIHLGYLETDRERGNDSFVSF---EEILEQALDQEVDMVLLGGDLFHINKPSP 78
+I+ +D+H R FV + + ++Q+ D++LLGGD + P
Sbjct: 50 FKILFLADLH-----YSR------FVPLSLISDAIALGIEQKPDLILLGGDYVLFDMPL- 97
Query: 79 TTLKKCLETLRKYCIGDRSVFIDVISDPKLVMCNDHVNYMDPNLNISLPVFTINGNHDDP 138
+ S F DV+S L C P F GNHD P
Sbjct: 98 ----------------NFSAFSDVLS--PLAEC--------------APTFACFGNHDRP 125
Query: 139 SGPE 142
G E
Sbjct: 126 VGTE 129
>gnl|CDD|129135 TIGR00024, SbcD_rel_arch, putative phosphoesterase,
SbcD/Mre11-related. Members of this uncharacterized
family share a motif approximating
DXH(X25)GDXXD(X25)GNHD as found in several
phosphoesterases, including the nucleases SbcD and
Mre11. SbcD is a subunit of the SbcCD nuclease of E.
coli that can cleave DNA hairpins to unblock stalled
DNA replication. All members of this family are
archaeal [Unknown function, Enzymes of unknown
specificity].
Length = 225
Score = 31.4 bits (71), Expect = 0.52
Identities = 17/59 (28%), Positives = 29/59 (49%), Gaps = 5/59 (8%)
Query: 23 RIMIASDIHLGYLETDRERG-NDSFVSFEEILEQALD----QEVDMVLLGGDLFHINKP 76
+ +D+HLG+ E+G F EI+E+AL ++ +++ GDL H K
Sbjct: 16 DKAVIADLHLGFERHLDEQGVMVPGFQFREIIERALSIADKYGIEALIINGDLKHEFKK 74
>gnl|CDD|224327 COG1409, Icc, Predicted phosphohydrolases [General function
prediction only].
Length = 301
Score = 31.1 bits (70), Expect = 0.62
Identities = 16/49 (32%), Positives = 24/49 (48%), Gaps = 6/49 (12%)
Query: 22 IRIMIASDIHLGYLETDRERGNDSFVSFEEILEQALDQEVDMVLLGGDL 70
+RI SD+HLG G DS E +L + D++++ GDL
Sbjct: 1 MRIAHISDLHLG------ALGVDSEELLEALLAAIEQLKPDLLVVTGDL 43
>gnl|CDD|216667 pfam01729, QRPTase_C, Quinolinate phosphoribosyl transferase,
C-terminal domain. Quinolinate phosphoribosyl
transferase (QPRTase) or nicotinate-nucleotide
pyrophosphorylase EC:2.4.2.19 is involved in the de novo
synthesis of NAD in both prokaryotes and eukaryotes. It
catalyzes the reaction of quinolinic acid with
5-phosphoribosyl-1-pyrophosphate (PRPP) in the presence
of Mg2+ to give rise to nicotinic acid mononucleotide
(NaMN), pyrophosphate and carbon dioxide. The QA
substrate is bound between the C-terminal domain of one
subunit, and the N-terminal domain of the other. The
C-terminal domain has a 7 beta-stranded TIM barrel-like
fold.
Length = 169
Score = 30.3 bits (69), Expect = 0.69
Identities = 12/43 (27%), Positives = 22/43 (51%), Gaps = 7/43 (16%)
Query: 47 VSFEEILEQALDQEVDMVLLGGDLFHINKPSPTTLKKCLETLR 89
V E LE+AL+ D+++L + SP +++ +E L
Sbjct: 87 VENLEELEEALEAGADIIML-------DNFSPEEVREAVEELD 122
>gnl|CDD|233408 TIGR01427, PTS_IIC_fructo, PTS system, fructose subfamily, IIC
component. This model represents the IIC component, or
IIC region of a IIABC or IIBC polypeptide of a
phosphotransferase system for carbohydrate transport.
Members of this family belong to the fructose-specific
subfamily of the broader family (pfam02378) of PTS IIC
proteins. Members should be found as part of the same
chain or in the same operon as fructose family IIA
(TIGR00848) and IIB (TIGR00829) protein regions. A
number of bacterial species have members in two
different branches of this subfamily, suggesting some
diversity in substrate specificity of its members.
Length = 346
Score = 30.5 bits (69), Expect = 1.0
Identities = 6/25 (24%), Positives = 12/25 (48%)
Query: 289 CGILMCNKQNYKLVPRSLETVRPFV 313
+ K K +P+SL ++P +
Sbjct: 121 YVVKGLQKYIKKKLPQSLRGLKPIL 145
>gnl|CDD|224325 COG1407, COG1407, Predicted ICC-like phosphoesterases [General
function prediction only].
Length = 235
Score = 30.4 bits (69), Expect = 1.0
Identities = 15/63 (23%), Positives = 29/63 (46%), Gaps = 5/63 (7%)
Query: 20 NTIRIMIASDIHLGYLETDRERG----NDSFVSFEEILEQALDQE-VDMVLLGGDLFHIN 74
R ++ +D+HLGY E+ RG + L++ +++ +++ GDL H
Sbjct: 18 PLGRTLVVADLHLGYEESLARRGINLPRYQTDRILKRLDRIIERYGPKRLIILGDLKHEF 77
Query: 75 KPS 77
S
Sbjct: 78 GKS 80
>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 = 29.3 bits (66), Expect = 1.8
Identities = 13/45 (28%), Positives = 19/45 (42%), Gaps = 6/45 (13%)
Query: 28 SDIHLGYLETDRERGNDSFVSFEEILEQALDQEVDMVLLGGDLFH 72
SD+HLG F+ + AL + + LL GD+F
Sbjct: 4 SDLHLG-----DGGPAADFLLLFLLAALALGEADALYLL-GDIFD 42
>gnl|CDD|220272 pfam09508, Lact_bio_phlase, Lacto-N-biose phosphorylase. The gene
which codes for this protein in gut-bacteria is located
in a novel putative operon for galactose metabolism. The
protein appears to be a carbohydrate-processing
phosphorolytic enzyme (EC:2.4.1.211), unlike either
glycoside hydrolases or glycoside lyase. Intestinal
colonisation by bifidobacteria is important for human
health, especially in pediatrics, because colonisation
seems to prevent infection by some pathogenic bacteria
that cause diarrhoea or other illnesses. The operon
seems to be involved in intestinal colonisation by
bifidobacteria mediated by metabolism of mucin sugars.
In addition, it may also resolve the question of the
nature of the bifidus factor in human milk as the
lacto-N-biose structure found in milk oligosaccharides.
Length = 716
Score = 30.1 bits (68), Expect = 1.8
Identities = 9/25 (36%), Positives = 19/25 (76%)
Query: 45 SFVSFEEILEQALDQEVDMVLLGGD 69
F+SF++ILE + +++D+++ GD
Sbjct: 482 EFISFDDILENGILEDIDVIINVGD 506
>gnl|CDD|213701 TIGR02336, TIGR02336, 1,3-beta-galactosyl-N-acetylhexosamine
phosphorylase. Members of this family are found in
phylogenetically diverse bacteria, including Clostridium
perfringens (in the Firmicutes), Bifidobacterium longum
and Propionibacterium acnes (in the Actinobacteria), and
Vibrio vulnificus (in the Proteobacteria), most of which
occur as mammalian pathogens or commensals. The nominal
activity, 1,3-beta-galactosyl-N-acetylhexosamine
phosphorylase (EC 2.4.1.211), varies somewhat from
instance to instance in relative rates for closely
related substrates [Energy metabolism, Biosynthesis and
degradation of polysaccharides].
Length = 719
Score = 29.9 bits (67), Expect = 2.0
Identities = 11/24 (45%), Positives = 20/24 (83%)
Query: 46 FVSFEEILEQALDQEVDMVLLGGD 69
F+SF++ILE +D ++D+++ GGD
Sbjct: 486 FISFDDILEHGIDSDIDVIINGGD 509
>gnl|CDD|227354 COG5021, HUL4, Ubiquitin-protein ligase [Posttranslational
modification, protein turnover, chaperones].
Length = 872
Score = 29.7 bits (67), Expect = 2.1
Identities = 10/95 (10%), Positives = 27/95 (28%), Gaps = 16/95 (16%)
Query: 205 KYMKPTDDKDIIYILVLHQNRPERGTVKNIAEDSIPSFFHFILWGHEHECRIKPEYNTKQ 264
+ + +D+ + V Q G + + + + + + F H K+
Sbjct: 421 QLGRESDESFYVASNVQQQRASREGPLLSGWKTRLNNLYRFYFVEH-----------RKK 469
Query: 265 RFHVCQPGSPVATSLCAGEAVQKKCGILMCNKQNY 299
SL + + + +K+
Sbjct: 470 TLTKNDSRLGSFISLNKLDIRR-----IKEDKRRK 499
>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 = 29.2 bits (66), Expect = 2.4
Identities = 16/56 (28%), Positives = 25/56 (44%), Gaps = 2/56 (3%)
Query: 20 NTIRIMIASDIHLGYLETDRERGNDSFVSFEEILEQALDQE-VDMVLLGGDLFHIN 74
+I+ +D+H G E E + +E+ LD E D+V+L GDL
Sbjct: 1 GKFKILQFADLHFGEGEGTCEGCEAD-LKTVAFIERVLDAEKPDLVVLTGDLITGE 55
>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 = 28.7 bits (65), Expect = 2.5
Identities = 14/50 (28%), Positives = 25/50 (50%), Gaps = 18/50 (36%)
Query: 23 RIMIASDIHLGYLETDRERGNDSFVSFEEILEQALD--QEVDMVLLGGDL 70
+I + SD H G+ E+LE+AL+ +VD+++ GD+
Sbjct: 1 KIGVISDTH----------GSL------ELLEKALELFGDVDLIIHAGDV 34
>gnl|CDD|239018 cd02067, B12-binding, B12 binding domain (B12-BD). This domain
binds different cobalamid derivates, like B12
(adenosylcobamide) or methylcobalamin or methyl-Co(III)
5-hydroxybenzimidazolylcobamide, it is found in several
enzymes, such as glutamate mutase, methionine synthase
and methylmalonyl-CoA mutase. Cobalamin undergoes a
conformational change on binding the protein; the
dimethylbenzimidazole group, which is coordinated to the
cobalt in the free cofactor, moves away from the corrin
and is replaced by a histidine contributed by the
protein. The sequence Asp-X-His-X-X-Gly, which contains
this histidine ligand, is conserved in many
cobalamin-binding proteins.
Length = 119
Score = 27.9 bits (63), Expect = 3.7
Identities = 15/55 (27%), Positives = 28/55 (50%), Gaps = 4/55 (7%)
Query: 46 FVSFEEILEQALDQEVDMVLLGGDLFHINKPSPTTLKKCLETLRKYCIGDRSVFI 100
V EEI+E A +++ D + L G + T +K+ +E L++ + D V +
Sbjct: 36 DVPPEEIVEAAKEEDADAIGLSG----LLTTHMTLMKEVIEELKEAGLDDIPVLV 86
>gnl|CDD|225040 COG2129, COG2129, Predicted phosphoesterases, related to the Icc
protein [General function prediction only].
Length = 226
Score = 28.5 bits (64), Expect = 4.1
Identities = 17/72 (23%), Positives = 31/72 (43%), Gaps = 14/72 (19%)
Query: 22 IRIMIASDIHLGYLETDRERGNDSFVSFEEILEQALDQEVDMVLLGGDL--FHINKPSPT 79
++I+ +D+H S S +++L A D D++++ GDL FH
Sbjct: 4 MKILAVTDLH------------GSEDSLKKLLNAAADIRADLLVIAGDLTYFHFGPKEVA 51
Query: 80 TLKKCLETLRKY 91
LE L++
Sbjct: 52 EELNKLEALKEL 63
>gnl|CDD|237868 PRK14960, PRK14960, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 702
Score = 28.5 bits (63), Expect = 5.2
Identities = 14/32 (43%), Positives = 19/32 (59%), Gaps = 2/32 (6%)
Query: 199 IKHNKVKYMKPTDDKDIIY--ILVLHQNRPER 228
+ H VK M D+ IIY IL +HQN+ E+
Sbjct: 231 VHHQDVKEMLGLIDRTIIYDLILAVHQNQREK 262
>gnl|CDD|234479 TIGR04123, P_estr_lig_assc, metallophosphoesterase, DNA
ligase-associated. Members of this protein family are
an uncharacterized putative metallophosphoesterase
associated with a DNA ligase, a helicase, and a
putative exonuclease. It may play a role in DNA repair.
Its system is present in about 12 % of prokaryotic
reference genomes.
Length = 208
Score = 27.9 bits (63), Expect = 5.3
Identities = 16/56 (28%), Positives = 29/56 (51%), Gaps = 7/56 (12%)
Query: 23 RIMIASDIHLGYLETDRERG-----NDSFVSFEEILEQALDQ-EVDMVLLGGDLFH 72
R+++ +D+HLG R RG D+ + E L + + + +++ GDLFH
Sbjct: 22 RLLVVADLHLGKAAHFRARGIPLPPYDTRATLER-LAALIQRYQPRRLIVLGDLFH 76
>gnl|CDD|239022 cd02071, MM_CoA_mut_B12_BD, methylmalonyl CoA mutase B12 binding
domain. This domain binds to B12 (adenosylcobamide),
which initiates the conversion of succinyl CoA and
methylmalonyl CoA by forming an adenosyl radical, which
then undergoes a rearrangement exchanging a hydrogen
atom with a group attached to a neighboring carbon
atom. This family is present in both mammals and
bacteria. Bacterial members are heterodimers and
involved in the fermentation of pyruvate to propionate.
Mammalian members are homodimers and responsible for
the conversion of odd-chain fatty acids and
branched-chain amino acids via propionyl CoA to
succinyl CoA for further degradation.
Length = 122
Score = 27.2 bits (61), Expect = 5.5
Identities = 18/54 (33%), Positives = 28/54 (51%), Gaps = 12/54 (22%)
Query: 50 EEILEQALDQEVDMV----LLGGDLFHINKPSPTTLKKCLETLRKYCIGDRSVF 99
EEI+E A+ ++VD++ L GG H+ T + +E LR+ GD V
Sbjct: 40 EEIVEAAIQEDVDVIGLSSLSGG---HM-----TLFPEVIELLRELGAGDILVV 85
>gnl|CDD|225096 COG2185, Sbm, Methylmalonyl-CoA mutase, C-terminal domain/subunit
(cobalamin-binding) [Lipid metabolism].
Length = 143
Score = 27.3 bits (61), Expect = 5.8
Identities = 13/51 (25%), Positives = 27/51 (52%), Gaps = 6/51 (11%)
Query: 46 FVSFEEILEQALDQEVDMVLLGG-DLFHINKPSPTTLKKCLETLRKYCIGD 95
F + EE + A++++VD++ + D H+ T + +E LR+ + D
Sbjct: 49 FQTPEEAVRAAVEEDVDVIGVSSLDGGHL-----TLVPGLVEALREAGVED 94
>gnl|CDD|220637 pfam10223, DUF2181, Uncharacterized conserved protein (DUF2181).
This is region of approximately 250 residues conserved
from worms to humans. Its function is unknown.
Length = 244
Score = 27.8 bits (62), Expect = 6.4
Identities = 15/44 (34%), Positives = 20/44 (45%), Gaps = 9/44 (20%)
Query: 25 MIASDIHLGYLETDRERG---------NDSFVSFEEILEQALDQ 59
MI +D+ LG L T ER S ++ EE LE+ L
Sbjct: 27 MIEADVLLGGLNTGNEREVPIMAHPPAIYSDITLEEWLEEVLKS 70
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
0.320 0.138 0.414
Gapped
Lambda K H
0.267 0.0663 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 15,843,194
Number of extensions: 1520416
Number of successful extensions: 1382
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1365
Number of HSP's successfully gapped: 48
Length of query: 313
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 216
Effective length of database: 6,635,264
Effective search space: 1433217024
Effective search space used: 1433217024
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: 59 (26.6 bits)