RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8633
(327 letters)
>gnl|CDD|163630 cd07387, MPP_PolD2_C, PolD2 (DNA polymerase delta, subunit 2),
C-terminal domain. PolD2 (DNA polymerase delta, subunit
2) is an auxiliary subunit of the eukaryotic DNA
polymerase delta (PolD) complex thought to play a
regulatory role and to serve as a scaffold for PolD
assembly by interacting simultaneously with all of the
other three subunits. PolD2 is catalytically inactive
and lacks the active site residues required for
phosphoesterase activity in other members of this
superfamily. PolD2 is also involved in the recruitment
of several proteins regulating DNA metabolism, including
p21, PDIP1, PDIP38, PDIP46, and WRN. Human PolD consists
of four subunits: p125 (PolD1), p50 (PolD2), p66(PolD3),
and p12(PolD4). PolD is one of three major replicases
in eukaryotes. PolD also plays an essential role in
translesion DNA synthesis, homologous recombination, and
DNA repair. Within the PolD complex, PolD2 tightly
associates with PolD3. PolD2 belongs to the
metallophosphatase (MPP) superfamily. MPPs are
functionally diverse, but 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 = 257
Score = 279 bits (716), Expect = 5e-94
Identities = 98/161 (60%), Positives = 120/161 (74%)
Query: 156 SSIEVDLMPGEFDPANTTLPQQPLHPCLFPEASKYSTFHPVTNPYIFEMEGKLLMGTSGQ 215
SS+ VDLMPGEFDPAN +LPQQPLH CLFP++S YST + VTNPY F ++G ++GTSGQ
Sbjct: 93 SSVPVDLMPGEFDPANHSLPQQPLHRCLFPKSSNYSTLNLVTNPYEFSIDGVRVLGTSGQ 152
Query: 216 PVSDIAKFSNLSNPLDILEYTLRCGHVAPTAPDTLACYPFYDNDPMIIESCPDVYFTGNQ 275
V DI K+S+L + LDILE TL+ H+APTAPDTL CYPF D DP I+E CP VYF GNQ
Sbjct: 153 NVDDILKYSSLESRLDILERTLKWRHIAPTAPDTLWCYPFTDRDPFILEECPHVYFAGNQ 212
Query: 276 SKFETKTIEIEKDKNVRLISVPDFFSSRTVAILNLSTLECH 316
KF TK +E E+ + V L+ VP F + T ++NL TLEC
Sbjct: 213 PKFGTKLVEGEEGQRVLLVCVPSFSKTGTAVLVNLRTLECE 253
Score = 51.5 bits (124), Expect = 2e-07
Identities = 21/49 (42%), Positives = 32/49 (65%), Gaps = 2/49 (4%)
Query: 2 IIESCPDVYFTGNQSKFETKTIEIEKGKSVSVLKLSDLNETDTEECVII 50
I+E CP VYF GNQ KF TK +E E+G+ V ++ + ++T T V++
Sbjct: 199 ILEECPHVYFAGNQPKFGTKLVEGEEGQRVLLVCVPSFSKTGT--AVLV 245
>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 = 133 bits (336), Expect = 6e-38
Identities = 51/129 (39%), Positives = 75/129 (58%), Gaps = 6/129 (4%)
Query: 155 HSSIEVDLMPGEFDPANTT-LPQQPLHPCLFPEASKYSTFHPVTNPYIFEMEGKLLMGTS 213
SS V L+PG DP N+T LPQ P CLFP++ KY++ VTNP F + G ++ TS
Sbjct: 57 LSSTPVILVPGPNDPTNSTVLPQPPFPRCLFPKSKKYNSLQFVTNPCRFSINGVEIVVTS 116
Query: 214 GQPVSDIAKFS-----NLSNPLDILEYTLRCGHVAPTAPDTLACYPFYDNDPMIIESCPD 268
G V D+ ++S + L ++E LR H+ P APDTL YP+ +DP +++ PD
Sbjct: 117 GDNVKDLLRYSLKFSSSEERLLRLVETILRQRHLYPLAPDTLGPYPYDKDDPFVLDPLPD 176
Query: 269 VYFTGNQSK 277
V+ G++
Sbjct: 177 VFIVGDKLP 185
>gnl|CDD|224230 COG1311, HYS2, Archaeal DNA polymerase II, small subunit/DNA
polymerase delta, subunit B [DNA replication,
recombination, and repair].
Length = 481
Score = 98.2 bits (245), Expect = 8e-23
Identities = 45/164 (27%), Positives = 72/164 (43%), Gaps = 11/164 (6%)
Query: 156 SSIEVDLMPGEFDPANTTLPQQPLHPCLFPEASKYSTF--HPVTNPYIFEMEGKLLMGTS 213
I+V +MPG D LPQ H + S +S V+NP + + G ++
Sbjct: 307 EHIKVFIMPGNHDAVRQALPQP--HFPELIK-SLFSLNNLLFVSNPALVSLHGVDVLIYH 363
Query: 214 GQPVSDIAKF---SNLSNPLDILEYTLRCGHVAPTAPDTLACYPFYDNDPMIIESCPDVY 270
G+ + DI K ++ +PL +E L+ H+APT TL P D ++IE PDV+
Sbjct: 364 GRSIDDIIKLVPGADYDSPLKAMEELLKRRHLAPTYGGTLPIAPETK-DYLVIEEVPDVF 422
Query: 271 FTGNQSKFETKTIEIEKDKNVRLISVPDFFSSRTVAILNLSTLE 314
TG+ KF T E V + + + + +N +
Sbjct: 423 HTGHVHKFGTGVYEGV--NLVNSGTWQEQTEFQKMVNINPTPGN 464
>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 = 46.5 bits (111), Expect = 5e-06
Identities = 34/156 (21%), Positives = 62/156 (39%), Gaps = 36/156 (23%)
Query: 156 SSIEVDLMPGEFDPANTTLPQQPLHPCLFPEASKY-STFHP-----VTNPYIFEMEGKLL 209
S I++ ++PG D PQ PE + F P V+NP + ++ G +
Sbjct: 80 SHIKIIIIPGNHDAVRQAEPQPA-----LPE--EIRKLFLPGNVEFVSNPALVKIHGVDV 132
Query: 210 MGTSGQPVSDIAKF---SNLSNPLDILEYTLRCGHVAPT-------APDTLACYPFYDND 259
+ G+ + D+ K + P +E L+ H+AP AP+ D
Sbjct: 133 LIYHGRSIDDVVKLIPGLSYDKPGKAMEELLKRRHLAPIYGGRTPIAPEP--------ED 184
Query: 260 PMIIESCPDVYFTGNQSKFETKTIEIEKDKNVRLIS 295
++I+ PD+ TG+ + + V L++
Sbjct: 185 YLVIDEVPDILHTGH-----VHVYGVGVYRGVLLVN 215
>gnl|CDD|235208 PRK04036, PRK04036, DNA polymerase II small subunit; Validated.
Length = 504
Score = 40.3 bits (95), Expect = 0.001
Identities = 45/191 (23%), Positives = 72/191 (37%), Gaps = 55/191 (28%)
Query: 158 IEVDLMPGEFDPANTTLPQQPLHPCLFPEASKYSTFHP------VTNPYIFEMEGKLLMG 211
I++ + PG D PQ P FPE + + P V+NP + + G ++
Sbjct: 331 IKIIISPGNHDAVRQAEPQ----PA-FPE--EIRSLFPEHNVTFVSNPALVNLHGVDVLI 383
Query: 212 TSGQPVSD-IAKFSNLS--NPLDILEYTLRCGHVAPT-------APDTLACYPFYDNDPM 261
G+ + D I+ S P +E L+ H+AP AP+ D +
Sbjct: 384 YHGRSIDDVISLIPGASYEKPGKAMEELLKRRHLAPIYGGRTPIAPE--------KEDYL 435
Query: 262 IIESCPDVYFTGNQSKFETKTIEIEKDKNVRLIS----------------VPDFFSSRTV 305
+I+ PD++ TG+ K + V LI+ VP V
Sbjct: 436 VIDEVPDIFHTGH-----VHINGYGKYRGVLLINSGTWQAQTEFQKRVNIVPT---PARV 487
Query: 306 AILNLSTLECH 316
I++L TLE
Sbjct: 488 PIVDLDTLEVT 498
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
0.316 0.135 0.395
Gapped
Lambda K H
0.267 0.0701 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 16,454,940
Number of extensions: 1566701
Number of successful extensions: 1225
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1218
Number of HSP's successfully gapped: 13
Length of query: 327
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 230
Effective length of database: 6,635,264
Effective search space: 1526110720
Effective search space used: 1526110720
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 (21.6 bits)
S2: 59 (26.6 bits)