RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2760
(333 letters)
>gnl|CDD|226947 COG4581, COG4581, Superfamily II RNA helicase [DNA replication,
recombination, and repair].
Length = 1041
Score = 125 bits (317), Expect = 6e-32
Identities = 51/89 (57%), Positives = 58/89 (65%), Gaps = 4/89 (4%)
Query: 180 FDAKVPI----MAHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQN 235
DA+ P A +PFELD FQ++AI LE V V A TS+GKTV+AEYAIAL+
Sbjct: 101 PDAESPFDLAPPAREYPFELDPFQQEAIAILERGESVLVCAPTSSGKTVVAEYAIALALR 160
Query: 236 HKTRTIYTSPIKALSNQKYRDFRETFQDV 264
R IYTSPIKALSNQKYRD F DV
Sbjct: 161 DGQRVIYTSPIKALSNQKYRDLLAKFGDV 189
>gnl|CDD|215832 pfam00270, DEAD, DEAD/DEAH box helicase. Members of this family
include the DEAD and DEAH box helicases. Helicases are
involved in unwinding nucleic acids. The DEAD box
helicases are involved in various aspects of RNA
metabolism, including nuclear transcription, pre mRNA
splicing, ribosome biogenesis, nucleocytoplasmic
transport, translation, RNA decay and organellar gene
expression.
Length = 169
Score = 56.9 bits (138), Expect = 7e-10
Identities = 20/71 (28%), Positives = 34/71 (47%), Gaps = 3/71 (4%)
Query: 199 QKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIA---LSQNHKTRTIYTSPIKALSNQKYR 255
Q QAI + V V A T +GKT+ I L + + + +P + L+ Q Y
Sbjct: 4 QAQAIPAILSGKDVLVQAPTGSGKTLAFLLPILQALLPKKGGPQALVLAPTRELAEQIYE 63
Query: 256 DFRETFQDVGL 266
+ ++ F+ +GL
Sbjct: 64 ELKKLFKILGL 74
>gnl|CDD|214692 smart00487, DEXDc, DEAD-like helicases superfamily.
Length = 201
Score = 51.0 bits (122), Expect = 1e-07
Identities = 21/79 (26%), Positives = 34/79 (43%), Gaps = 3/79 (3%)
Query: 192 PFELDVFQKQAI-IKLEEHNHVFVTAHTSAGKTVIAEYAI--ALSQNHKTRTIYTSPIKA 248
L +QK+AI L V + A T +GKT+ A AL + R + P +
Sbjct: 6 FEPLRPYQKEAIEALLSGLRDVILAAPTGSGKTLAALLPALEALKRGKGGRVLVLVPTRE 65
Query: 249 LSNQKYRDFRETFQDVGLI 267
L+ Q + ++ +GL
Sbjct: 66 LAEQWAEELKKLGPSLGLK 84
>gnl|CDD|224123 COG1202, COG1202, Superfamily II helicase, archaea-specific
[General function prediction only].
Length = 830
Score = 51.3 bits (123), Expect = 4e-07
Identities = 25/62 (40%), Positives = 39/62 (62%), Gaps = 2/62 (3%)
Query: 206 LEEHNHVFVTAHTSAGKTVIAEYA-IALSQNHKTRTIYTSPIKALSNQKYRDFRETFQDV 264
LE N + V+A T++GKT+I E A I + + ++ P+ AL+NQKY DF+E + +
Sbjct: 230 LEGENLLVVSA-TASGKTLIGELAGIPRLLSGGKKMLFLVPLVALANQKYEDFKERYSKL 288
Query: 265 GL 266
GL
Sbjct: 289 GL 290
>gnl|CDD|224125 COG1204, COG1204, Superfamily II helicase [General function
prediction only].
Length = 766
Score = 49.7 bits (119), Expect = 1e-06
Identities = 21/55 (38%), Positives = 32/55 (58%), Gaps = 3/55 (5%)
Query: 206 LEEHNHVFVTAHTSAGKTVIAEYAIALS--QNHKTRTIYTSPIKALSNQKYRDFR 258
L +V ++A T +GKT+IA AI LS + +Y P+KAL+ +KY +F
Sbjct: 44 LLSDENVLISAPTGSGKTLIALLAI-LSTLLEGGGKVVYIVPLKALAEEKYEEFS 97
>gnl|CDD|100801 PRK01172, PRK01172, ski2-like helicase; Provisional.
Length = 674
Score = 46.4 bits (110), Expect = 1e-05
Identities = 24/65 (36%), Positives = 40/65 (61%)
Query: 193 FELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQ 252
FEL Q+ AI +L + +V V+ T+AGKT+IA AI + ++IY P+++L+ +
Sbjct: 21 FELYDHQRMAIEQLRKGENVIVSVPTAAGKTLIAYSAIYETFLAGLKSIYIVPLRSLAME 80
Query: 253 KYRDF 257
KY +
Sbjct: 81 KYEEL 85
>gnl|CDD|224126 COG1205, COG1205, Distinct helicase family with a unique C-terminal
domain including a metal-binding cysteine cluster
[General function prediction only].
Length = 851
Score = 45.5 bits (108), Expect = 3e-05
Identities = 20/70 (28%), Positives = 30/70 (42%), Gaps = 2/70 (2%)
Query: 198 FQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAI--ALSQNHKTRTIYTSPIKALSNQKYR 255
Q A+ + E +V VT T +GKT I L ++ R + P AL+N +
Sbjct: 74 HQVDALRLIREGRNVVVTTGTGSGKTESFLLPILDHLLRDPSARALLLYPTNALANDQAE 133
Query: 256 DFRETFQDVG 265
RE D+
Sbjct: 134 RLRELISDLP 143
>gnl|CDD|238005 cd00046, DEXDc, DEAD-like helicases superfamily. A diverse family
of proteins involved in ATP-dependent RNA or DNA
unwinding. This domain contains the ATP-binding region.
Length = 144
Score = 40.0 bits (94), Expect = 3e-04
Identities = 19/82 (23%), Positives = 32/82 (39%), Gaps = 5/82 (6%)
Query: 210 NHVFVTAHTSAGKTVIAEYAI--ALSQNHKTRTIYTSPIKALSNQKYRDFRETFQ---DV 264
V + A T +GKT+ A I L + + +P + L+NQ +E F V
Sbjct: 1 RDVLLAAPTGSGKTLAALLPILELLDSLKGGQVLVLAPTRELANQVAERLKELFGEGIKV 60
Query: 265 GLIDDLPPVFPDVEKLLEDLNI 286
G + + + L +I
Sbjct: 61 GYLIGGTSIKQQEKLLSGKTDI 82
>gnl|CDD|218292 pfam04851, ResIII, Type III restriction enzyme, res subunit.
Length = 100
Score = 38.0 bits (89), Expect = 7e-04
Identities = 17/54 (31%), Positives = 26/54 (48%)
Query: 199 QKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQ 252
Q++AI +L E + T +GKT+ A IA K + ++ P K L Q
Sbjct: 8 QEEAIERLLEKKRGLIVMATGSGKTLTAAALIARLAKGKKKVLFVVPRKDLLEQ 61
>gnl|CDD|234478 TIGR04121, DEXH_lig_assoc, DEXH box helicase, DNA
ligase-associated. Members of this protein family are
DEAD/DEAH box helicases found associated with a
bacterial ATP-dependent DNA ligase, part of a four-gene
system that occurs in about 12 % of prokaryotic
reference genomes. The actual motif in this family is
DE[VILW]H.
Length = 803
Score = 39.5 bits (93), Expect = 0.002
Identities = 17/75 (22%), Positives = 32/75 (42%), Gaps = 6/75 (8%)
Query: 198 FQKQAIIKLEEHNHVFVTAHTSAGKT------VIAEYAIALSQNHKTRTIYTSPIKALSN 251
FQ + E + A T +GKT + + A T+Y +P++AL+
Sbjct: 17 FQLEMWAAALEGRSGLLIAPTGSGKTLAGFLPSLIDLAGPEKPKKGLHTLYITPLRALAV 76
Query: 252 QKYRDFRETFQDVGL 266
R+ + +++GL
Sbjct: 77 DIARNLQAPIEELGL 91
>gnl|CDD|234702 PRK00254, PRK00254, ski2-like helicase; Provisional.
Length = 720
Score = 39.0 bits (91), Expect = 0.003
Identities = 19/52 (36%), Positives = 35/52 (67%), Gaps = 6/52 (11%)
Query: 218 TSAGKTVIAEYAIA---LSQNHKTRTIYTSPIKALSNQKYRDFRETFQDVGL 266
T++GKT++AE + L + K +Y P+KAL+ +KYR+F++ ++ +GL
Sbjct: 48 TASGKTLVAEIVMVNKLLREGGKA--VYLVPLKALAEEKYREFKD-WEKLGL 96
>gnl|CDD|235032 PRK02362, PRK02362, ski2-like helicase; Provisional.
Length = 737
Score = 38.0 bits (89), Expect = 0.006
Identities = 16/49 (32%), Positives = 34/49 (69%), Gaps = 1/49 (2%)
Query: 218 TSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQDVGL 266
T++GKT+IAE A+ + + +Y P++AL+++K+ +F F+++G+
Sbjct: 48 TASGKTLIAELAMLKAIARGGKALYIVPLRALASEKFEEFER-FEELGV 95
>gnl|CDD|224122 COG1201, Lhr, Lhr-like helicases [General function prediction
only].
Length = 814
Score = 36.9 bits (86), Expect = 0.013
Identities = 17/61 (27%), Positives = 27/61 (44%), Gaps = 8/61 (13%)
Query: 199 QKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAI--------ALSQNHKTRTIYTSPIKALS 250
Q+ AI ++ +V + A T +GKT A + +Y SP+KAL+
Sbjct: 27 QRYAIPEIHSGENVLIIAPTGSGKTEAAFLPVINELLSLGKGKLEDGIYALYISPLKALN 86
Query: 251 N 251
N
Sbjct: 87 N 87
>gnl|CDD|237497 PRK13767, PRK13767, ATP-dependent helicase; Provisional.
Length = 876
Score = 34.9 bits (81), Expect = 0.058
Identities = 22/70 (31%), Positives = 37/70 (52%), Gaps = 9/70 (12%)
Query: 199 QKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAI-----ALSQN----HKTRTIYTSPIKAL 249
Q+ AI + E +V +++ T +GKT+ A AI L + K +Y SP++AL
Sbjct: 37 QRYAIPLIHEGKNVLISSPTGSGKTLAAFLAIIDELFRLGREGELEDKVYCLYVSPLRAL 96
Query: 250 SNQKYRDFRE 259
+N +R+ E
Sbjct: 97 NNDIHRNLEE 106
>gnl|CDD|222875 PHA02558, uvsW, UvsW helicase; Provisional.
Length = 501
Score = 33.4 bits (77), Expect = 0.18
Identities = 16/64 (25%), Positives = 33/64 (51%), Gaps = 3/64 (4%)
Query: 198 FQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIAL--SQNHKTRTIYTSPIKALSNQKYR 255
+Q A+ + ++N + TSAGK++I Y ++ +N++ + + P +L Q
Sbjct: 118 YQYDAVYEGLKNNRRLLNLPTSAGKSLIQ-YLLSRYYLENYEGKVLIIVPTTSLVTQMID 176
Query: 256 DFRE 259
DF +
Sbjct: 177 DFVD 180
>gnl|CDD|187770 cd09639, Cas3_I, CRISPR/Cas system-associated protein Cas3. CRISPR
(Clustered Regularly Interspaced Short Palindromic
Repeats) and associated Cas proteins comprise a system
for heritable host defense by prokaryotic cells against
phage and other foreign DNA; DEAD/DEAH box helicase DNA
helicase cas3'; Often but not always is fused to HD
nuclease domain; signature gene for Type I.
Length = 353
Score = 32.4 bits (74), Expect = 0.29
Identities = 19/58 (32%), Positives = 24/58 (41%), Gaps = 4/58 (6%)
Query: 212 VFVTAHTSAGKTVIAEYAIALSQNHKT---RTIYTSPIKALSNQKYRDFRETFQDVGL 266
+ + A T GKT A AL R I P +A N YR +E F + GL
Sbjct: 2 LVIEAPTGYGKTEAA-LLWALHSLKSQKADRVIIALPTRATINAMYRRAKEAFGETGL 58
>gnl|CDD|234365 TIGR03817, DECH_helic, helicase/secretion neighborhood putative
DEAH-box helicase. A conserved gene neighborhood widely
spread in the Actinobacteria contains this
uncharacterized DEAH-box family helicase encoded
convergently towards an operon of genes for protein
homologous to type II secretion and pilus formation
proteins. The context suggests that this helicase may
play a role in conjugal transfer of DNA.
Length = 742
Score = 30.5 bits (69), Expect = 1.3
Identities = 16/51 (31%), Positives = 29/51 (56%), Gaps = 2/51 (3%)
Query: 211 HVFVTAHTSAGKTVIAEYAI--ALSQNHKTRTIYTSPIKALSNQKYRDFRE 259
HV V T++GK++ + + AL+ + + +Y +P KAL+ + R RE
Sbjct: 53 HVVVATGTASGKSLAYQLPVLSALADDPRATALYLAPTKALAADQLRAVRE 103
>gnl|CDD|225083 COG2172, RsbW, Anti-sigma regulatory factor (Ser/Thr protein
kinase) [Signal transduction mechanisms].
Length = 146
Score = 29.3 bits (66), Expect = 1.5
Identities = 13/32 (40%), Positives = 15/32 (46%)
Query: 38 ITILDPGPRIDDLPPVFPDVEKLLEDLNIGGL 69
I I D GP I+DL + E L GGL
Sbjct: 79 IRIWDQGPGIEDLEESLGPGDTTAEGLQEGGL 110
>gnl|CDD|234667 PRK00149, dnaA, chromosomal replication initiation protein;
Reviewed.
Length = 401
Score = 29.7 bits (68), Expect = 2.2
Identities = 19/62 (30%), Positives = 28/62 (45%), Gaps = 15/62 (24%)
Query: 221 GKT----VIAEYAIALSQNHKTRTIYTSP-------IKALSNQKYRDFRETFQ--DVGLI 267
GKT I Y L +N + +Y + + AL N +F+E ++ DV LI
Sbjct: 111 GKTHLLHAIGNYI--LEKNPNAKVVYVTSEKFTNDFVNALRNNTMEEFKEKYRSVDVLLI 168
Query: 268 DD 269
DD
Sbjct: 169 DD 170
>gnl|CDD|151398 pfam10951, DUF2776, Protein of unknown function (DUF2776). This
bacterial family of proteins has no known function.
Length = 347
Score = 29.7 bits (67), Expect = 2.3
Identities = 17/60 (28%), Positives = 24/60 (40%), Gaps = 9/60 (15%)
Query: 186 IMAHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIAL--SQNHKTRTIYT 243
++A W F L + +EH FV H AG I IAL + + R Y+
Sbjct: 166 LIAWIWAFTL-------LAHSDEHPAYFVAGHVMAGLACICTSLIALVATIARQIRNTYS 218
>gnl|CDD|233063 TIGR00631, uvrb, excinuclease ABC, B subunit. All proteins in this
family for wich functions are known are DNA helicases
that function in the nucleotide excision repair and are
endonucleases that make the 3' incision next to DNA
damage. They are part of a pathway requiring UvrA, UvrB,
UvrC, and UvrD homologs. 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 = 655
Score = 29.6 bits (67), Expect = 2.5
Identities = 22/76 (28%), Positives = 32/76 (42%), Gaps = 24/76 (31%)
Query: 199 QKQAIIKLEE-----HNHVFVTAHTSAGKT-----VIAEY---AIALSQNHKTRTIYTSP 245
Q +AI KL E H + T +GKT VIA+ + ++ N
Sbjct: 14 QPKAIAKLVEGLTDGEKHQTLLGVTGSGKTFTMANVIAQVNRPTLVIAHN---------- 63
Query: 246 IKALSNQKYRDFRETF 261
K L+ Q Y +F+E F
Sbjct: 64 -KTLAAQLYNEFKEFF 78
>gnl|CDD|233483 TIGR01587, cas3_core, CRISPR-associated helicase Cas3. This model
represents the highly conserved core region of an
alignment of Cas3, a protein found in association with
CRISPR repeat elements in a broad range of bacteria and
archaea. Cas3 appears to be a helicase, with regions
found by pfam00270 (DEAD/DEAH box helicase) and
pfam00271 (Helicase conserved C-terminal domain). Some
but not all members have an N-terminal HD domain region
(pfam01966) that is not included within this model
[Mobile and extrachromosomal element functions, Other].
Length = 358
Score = 29.0 bits (65), Expect = 3.3
Identities = 17/55 (30%), Positives = 21/55 (38%), Gaps = 4/55 (7%)
Query: 212 VFVTAHTSAGKTVIAEYAIALSQNHKT---RTIYTSPIKALSNQKYRDFRETFQD 263
+ + A T GKT A AL R I P +A N YR +E F
Sbjct: 2 LVIEAPTGYGKTEAA-LLWALHSIKSQKADRVIIALPTRATINAMYRRAKELFGS 55
>gnl|CDD|217755 pfam03837, RecT, RecT family. The DNA single-strand annealing
proteins (SSAPs), such as RecT, Red-beta, ERF and Rad52,
function in RecA-dependent and RecA-independent DNA
recombination pathways. This family includes proteins
related to RecT.
Length = 193
Score = 28.5 bits (64), Expect = 3.8
Identities = 15/68 (22%), Positives = 23/68 (33%), Gaps = 11/68 (16%)
Query: 82 KFWKPKVQLVAGIINLIQLGGENASKFEQ--GLWESHEVISGDAKEEQ----EKATVFPS 135
+ + QL G I+L A + Q G+W V GD E +
Sbjct: 47 PYGGYEAQLQVGYKGFIKL----AKRSGQYAGIWA-GVVYEGDEFEYDRGKETEEVHGFF 101
Query: 136 NEEENNVI 143
+E +I
Sbjct: 102 EDERGELI 109
>gnl|CDD|232941 TIGR00362, DnaA, chromosomal replication initiator protein DnaA.
DnaA is involved in DNA biosynthesis; initiation of
chromosome replication and can also be transcription
regulator. The C-terminal of the family hits the pfam
bacterial DnaA (bac_dnaA) domain family. For a review,
see Kaguni (2006) [DNA metabolism, DNA replication,
recombination, and repair].
Length = 405
Score = 29.0 bits (66), Expect = 3.8
Identities = 15/48 (31%), Positives = 23/48 (47%), Gaps = 9/48 (18%)
Query: 231 ALSQNHKTRTIYTSP-------IKALSNQKYRDFRETFQ--DVGLIDD 269
L N + +Y S + AL N K +F+E ++ D+ LIDD
Sbjct: 160 ILENNPNAKVVYVSSEKFTNDFVNALRNNKMEEFKEKYRSVDLLLIDD 207
>gnl|CDD|236578 PRK09583, PRK09583, mycothiol-dependent maleylpyruvate isomerase;
Reviewed.
Length = 241
Score = 28.5 bits (64), Expect = 4.3
Identities = 11/24 (45%), Positives = 13/24 (54%), Gaps = 2/24 (8%)
Query: 41 LDPGPRIDDLPPVFPDVEKLLEDL 64
L G DLP VF VE+LL +
Sbjct: 153 LGAGYTFADLPEVF--VERLLAWI 174
>gnl|CDD|113530 pfam04763, DUF562, Protein of unknown function (DUF562). Family
of uncharacterized proteins.
Length = 146
Score = 27.8 bits (62), Expect = 4.5
Identities = 12/38 (31%), Positives = 17/38 (44%), Gaps = 2/38 (5%)
Query: 37 VITILDPGPRIDDLPPVFPDVEKLLEDLNIGGLDELSI 74
V+ P + LPP V L+E+L G L+I
Sbjct: 19 VVVCNHSTPGPESLPP--ESVSLLIEELEESGYSYLNI 54
>gnl|CDD|200463 cd11324, AmyAc_Amylosucrase, Alpha amylase catalytic domain found
in Amylosucrase. Amylosucrase is a glucosyltransferase
that catalyzes the transfer of a D-glucopyranosyl moiety
from sucrose onto an acceptor molecule. When the
acceptor is another saccharide, only alpha-1,4 linkages
are produced. Unlike most amylopolysaccharide synthases,
it does not require any alpha-D-glucosyl nucleoside
diphosphate substrate. In the presence of glycogen it
catalyzes the transfer of a D-glucose moiety onto a
glycogen branch, but in its absence, it hydrolyzes
sucrose and synthesizes polymers, smaller
maltosaccharides, and sucrose isoforms. The
Alpha-amylase family comprises the largest family of
glycoside hydrolases (GH), with the majority of enzymes
acting on starch, glycogen, and related oligo- and
polysaccharides. These proteins catalyze the
transformation of alpha-1,4 and alpha-1,6 glucosidic
linkages with retention of the anomeric center. The
protein is described as having 3 domains: A, B, C. A is
a (beta/alpha) 8-barrel; B is a loop between the beta 3
strand and alpha 3 helix of A; C is the C-terminal
extension characterized by a Greek key. The majority of
the enzymes have an active site cleft found between
domains A and B where a triad of catalytic residues
(Asp, Glu and Asp) performs catalysis. Other members of
this family have lost the catalytic activity as in the
case of the human 4F2hc, or only have 2 residues that
serve as the catalytic nucleophile and the acid/base,
such as Thermus A4 beta-galactosidase with 2 Glu
residues (GH42) and human alpha-galactosidase with 2 Asp
residues (GH31). The family members are quite extensive
and include: alpha amylase, maltosyltransferase,
cyclodextrin glycotransferase, maltogenic amylase,
neopullulanase, isoamylase, 1,4-alpha-D-glucan
maltotetrahydrolase, 4-alpha-glucotransferase,
oligo-1,6-glucosidase, amylosucrase, sucrose
phosphorylase, and amylomaltase.
Length = 536
Score = 28.7 bits (65), Expect = 4.5
Identities = 14/36 (38%), Positives = 19/36 (52%), Gaps = 5/36 (13%)
Query: 247 KALS-NQKYRDFRETFQDVGLID----DLPPVFPDV 277
KA + + +Y+D+ F D L D LP VFPD
Sbjct: 170 KARAGDPEYQDYYYMFPDRTLPDAYERTLPEVFPDT 205
>gnl|CDD|137505 PRK09751, PRK09751, putative ATP-dependent helicase Lhr;
Provisional.
Length = 1490
Score = 28.7 bits (64), Expect = 4.8
Identities = 19/65 (29%), Positives = 28/65 (43%), Gaps = 13/65 (20%)
Query: 214 VTAHTSAGKTVIA----------EYAIALSQNHK---TRTIYTSPIKALSNQKYRDFRET 260
V A T +GKT+ A E + HK +R +Y SPIKAL R+ +
Sbjct: 1 VIAPTGSGKTLAAFLYALDRLFREGGEDTREAHKRKTSRILYISPIKALGTDVQRNLQIP 60
Query: 261 FQDVG 265
+ +
Sbjct: 61 LKGIA 65
>gnl|CDD|176453 cd00424, PolY, Y-family of DNA polymerases. Y-family DNA
polymerases are a specialized subset of polymerases that
facilitate translesion synthesis (TLS), a process that
allows the bypass of a variety of DNA lesions. Unlike
replicative polymerases, TLS polymerases lack
proofreading activity and have low fidelity and low
processivity. They use damaged DNA as templates and
insert nucleotides opposite the lesions. The active
sites of TLS polymerases are large and flexible to allow
the accomodation of distorted bases. Most TLS
polymerases are members of the Y-family, including Pol
eta, Pol kappa/IV, Pol iota, Rev1, and Pol V, which is
found exclusively in bacteria. In eukaryotes, the
B-family polymerase Pol zeta also functions as a TLS
polymerase. Expression of Y-family polymerases is often
induced by DNA damage and is believed to be highly
regulated. TLS is likely induced by the
monoubiquitination of the replication clamp PCNA, which
provides a scaffold for TLS polymerases to bind in order
to access the lesion. Because of their high error
rates, TLS polymerases are potential targets for cancer
treatment and prevention.
Length = 343
Score = 27.7 bits (62), Expect = 9.4
Identities = 16/57 (28%), Positives = 23/57 (40%), Gaps = 8/57 (14%)
Query: 36 DVITILDPGP--------RIDDLPPVFPDVEKLLEDLNIGGLDELSIHDFNKHLKFW 84
D +TILDP + DLP + K LE + I + +L + L W
Sbjct: 156 DGLTILDPEDLPGFLSKLPLTDLPGIGAVTAKRLEAVGINPIGDLLAASPDALLALW 212
>gnl|CDD|238540 cd01120, RecA-like_NTPases, RecA-like NTPases. This family includes
the NTP binding domain of F1 and V1 H+ATPases, DnaB and
related helicases as well as bacterial RecA and related
eukaryotic and archaeal recombinases. This group also
includes bacterial conjugation proteins and related DNA
transfer proteins involved in type II and type IV
secretion.
Length = 165
Score = 27.1 bits (60), Expect = 9.5
Identities = 9/50 (18%), Positives = 17/50 (34%)
Query: 211 HVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRET 260
+ V T +GKT +A + +Y + + R E+
Sbjct: 1 LILVFGPTGSGKTTLALQLALNIATKGGKVVYVDIEEEIEELTERLIGES 50
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 0.411
Gapped
Lambda K H
0.267 0.0643 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 17,443,335
Number of extensions: 1717948
Number of successful extensions: 1560
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1549
Number of HSP's successfully gapped: 46
Length of query: 333
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 236
Effective length of database: 6,635,264
Effective search space: 1565922304
Effective search space used: 1565922304
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: 59 (26.7 bits)