RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy151
(110 letters)
>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 = 72.7 bits (179), Expect = 2e-17
Identities = 27/92 (29%), Positives = 39/92 (42%), Gaps = 5/92 (5%)
Query: 18 PWVLDISGVVVGVTSVDVLMHLGREEFAAAPEMTDRLSRLASHLLQQQCYYPLIPPNVEL 77
P I+GV + VTS D + L R +RL RL +L+Q+ YPL P+
Sbjct: 102 PCRFSINGVEIVVTSGDNVKDLLRYSLKF-SSSEERLLRLVETILRQRHLYPL-APDTLG 159
Query: 78 PVDMECWELHA-QLPVTPHIMILPSDLRYFVK 108
P + + L P + I+ L FV
Sbjct: 160 PYPYD--KDDPFVLDPLPDVFIVGDKLPPFVT 189
>gnl|CDD|227539 COG5214, POL12, DNA polymerase alpha-primase complex,
polymerase-associated subunit B [DNA replication,
recombination, and repair].
Length = 581
Score = 68.9 bits (168), Expect = 5e-15
Identities = 28/103 (27%), Positives = 49/103 (47%), Gaps = 12/103 (11%)
Query: 16 PRPWVLDISGVVVGVTSVDVLMHLGREEF--AAAPEMTDRLSRLASHLLQQQCYYPLIPP 73
P I+ ++ G++S+D + + EE + DRL R++ HLL Q+ +YP+ P
Sbjct: 423 GNPCEFFINEILFGISSLDTPLEISSEECFHDSLLSGGDRLGRISYHLLFQRTFYPVFPG 482
Query: 74 NVEL---PVDMECWELHAQLP-----VTPHIMILPSDLRYFVK 108
P ++ + LP P I I+PS L++F +
Sbjct: 483 GSLEKCNPSSLDV--VSLSLPEFMSMTAPDIYIVPSKLKHFCR 523
>gnl|CDD|198067 smart00999, Aerolysin, Aerolysin toxin. This family represents the
pore forming lobe of aerolysin.
Length = 368
Score = 29.1 bits (65), Expect = 0.39
Identities = 6/43 (13%), Positives = 15/43 (34%), Gaps = 1/43 (2%)
Query: 63 QQQCYYPLIPPNVELPVDMECWELHAQLPVTPHIMILPSDLRY 105
Y +P + P+ +E ++ P + D+ +
Sbjct: 181 LSAQYRATMPARSKRPIKIELYKQKIDYPYESK-ADISYDVTF 222
>gnl|CDD|200559 cd10933, CE4_u9, Putative catalytic domain of uncharacterized
bacterial proteins from the carbohydrate esterase 4
superfamily. This family corresponds to a group of
uncharacterized bacterial proteins with high sequence
similarity to the catalytic domain of the six-stranded
barrel rhizobial NodB-like proteins, which remove
N-linked or O-linked acetyl groups from cell wall
polysaccharides and belong to the larger carbohydrate
esterase 4 (CE4) superfamily.
Length = 266
Score = 25.7 bits (57), Expect = 4.7
Identities = 7/24 (29%), Positives = 7/24 (29%)
Query: 74 NVELPVDMECWELHAQLPVTPHIM 97
V L VD E W A
Sbjct: 1 RVLLTVDTELWPNGANRDDQKFPP 24
>gnl|CDD|182860 PRK10949, PRK10949, protease 4; Provisional.
Length = 618
Score = 26.2 bits (58), Expect = 5.0
Identities = 16/36 (44%), Positives = 22/36 (61%), Gaps = 4/36 (11%)
Query: 20 VLDISGVVVGVTSV-DVLMHLGREEFAAAPEMTDRL 54
+LDISGV+V S + L LGR+ A+ +DRL
Sbjct: 60 LLDISGVIVDKPSSSNKLSQLGRQLLGAS---SDRL 92
>gnl|CDD|240270 PTZ00107, PTZ00107, hexokinase; Provisional.
Length = 464
Score = 25.8 bits (57), Expect = 5.4
Identities = 12/35 (34%), Positives = 18/35 (51%), Gaps = 9/35 (25%)
Query: 66 CYYPLIPPNVE------LPVDMECWELHAQLPVTP 94
CY+ P V P++MEC ++LP+TP
Sbjct: 251 CYFE---PEVSAYGYAGTPINMECGNFDSKLPITP 282
>gnl|CDD|176228 cd08267, MDR1, Medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family.
This group is a member of the medium chain
dehydrogenases/reductase (MDR)/zinc-dependent alcohol
dehydrogenase-like family, but lacks the zinc-binding
sites of the zinc-dependent alcohol dehydrogenases. The
medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family,
which contains the zinc-dependent alcohol dehydrogenase
(ADH-Zn) and related proteins, is a diverse group of
proteins related to the first identified member, class
I mammalian ADH. MDRs display a broad range of
activities and are distinguished from the smaller short
chain dehydrogenases (~ 250 amino acids vs. the ~ 350
amino acids of the MDR). The MDR proteins have 2
domains: a C-terminal NAD(P)-binding Rossmann fold
domain of a beta-alpha form and an N-terminal catalytic
domain with distant homology to GroES. The MDR group
contains a host of activities, including the founding
alcohol dehydrogenase (ADH), quinone reductase,
sorbitol dehydrogenase, formaldehyde dehydrogenase,
butanediol DH, ketose reductase, cinnamyl reductase,
and numerous others. The zinc-dependent alcohol
dehydrogenases (ADHs) catalyze the NAD(P)(H)-dependent
interconversion of alcohols to aldehydes or ketones.
Active site zinc has a catalytic role, while structural
zinc aids in stability. ADH-like proteins typically
form dimers (typically higher plants, mammals) or
tetramers (yeast, bacteria), and generally have 2
tightly bound zinc atoms per subunit. The active site
zinc is coordinated by a histidine, two cysteines, and
a water molecule. The second zinc seems to play a
structural role, affects subunit interactions, and is
typically coordinated by 4 cysteines.
Length = 319
Score = 25.6 bits (57), Expect = 6.1
Identities = 12/39 (30%), Positives = 16/39 (41%), Gaps = 2/39 (5%)
Query: 15 KPRPWVL--DISGVVVGVTSVDVLMHLGREEFAAAPEMT 51
+P P + D +G VV V S +G E F P
Sbjct: 56 RPFPPIPGMDFAGEVVAVGSGVTRFKVGDEVFGRLPPKG 94
>gnl|CDD|131292 TIGR02238, recomb_DMC1, meiotic recombinase Dmc1. This model
describes DMC1, a subfamily of a larger family of DNA
repair and recombination proteins. It is eukaryotic only
and most closely related to eukaryotic RAD51. It also
resembles archaeal RadA (TIGR02236) and RadB (TIGR02237)
and bacterial RecA (TIGR02012). It has been
characterized for human as a recombinase active only in
meiosis.
Length = 313
Score = 25.1 bits (55), Expect = 8.1
Identities = 11/29 (37%), Positives = 18/29 (62%)
Query: 33 VDVLMHLGREEFAAAPEMTDRLSRLASHL 61
VD +M L R +F+ E+++R +LA L
Sbjct: 197 VDSIMALFRVDFSGRGELSERQQKLAQML 225
>gnl|CDD|237585 PRK14015, pepN, aminopeptidase N; Provisional.
Length = 875
Score = 25.1 bits (56), Expect = 9.4
Identities = 12/39 (30%), Positives = 16/39 (41%), Gaps = 9/39 (23%)
Query: 36 LMHLGREE--------FAAAPEMTDRLSRLASHLLQQQC 66
L EE F A MTDRL+ L++ L+
Sbjct: 692 LAAADDEEAAELAEAQFDQADNMTDRLAALSA-LVNADL 729
>gnl|CDD|240294 PTZ00150, PTZ00150, phosphoglucomutase-2-like protein; Provisional.
Length = 584
Score = 25.0 bits (55), Expect = 9.6
Identities = 8/38 (21%), Positives = 12/38 (31%)
Query: 39 LGREEFAAAPEMTDRLSRLASHLLQQQCYYPLIPPNVE 76
L + A + L L Q Y L+P +
Sbjct: 547 LSGTKDEAVEKELAALVDEVVEQLMQPEKYGLVPRKED 584
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
0.321 0.136 0.417
Gapped
Lambda K H
0.267 0.0604 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,704,359
Number of extensions: 486642
Number of successful extensions: 470
Number of sequences better than 10.0: 1
Number of HSP's gapped: 466
Number of HSP's successfully gapped: 22
Length of query: 110
Length of database: 10,937,602
Length adjustment: 74
Effective length of query: 36
Effective length of database: 7,655,406
Effective search space: 275594616
Effective search space used: 275594616
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 (21.9 bits)
S2: 53 (24.5 bits)