RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3306
(535 letters)
>gnl|CDD|238827 cd01650, RT_nLTR_like, RT_nLTR: Non-LTR (long terminal repeat)
retrotransposon and non-LTR retrovirus reverse
transcriptase (RT). This subfamily contains both non-LTR
retrotransposons and non-LTR retrovirus RTs. RTs
catalyze the conversion of single-stranded RNA into
double-stranded DNA for integration into host
chromosomes. RT is a multifunctional enzyme with
RNA-directed DNA polymerase, DNA directed DNA polymerase
and ribonuclease hybrid (RNase H) activities.
Length = 220
Score = 74.6 bits (184), Expect = 3e-15
Identities = 31/123 (25%), Positives = 62/123 (50%), Gaps = 17/123 (13%)
Query: 44 GIPQGGVASSTLFAIAINTITSYI---------HPSLSSSLFVDDFAIFTRDKNKDLLIS 94
G+ QG S LF +A++ + + P ++ + DD +F+ K++
Sbjct: 106 GVRQGDPLSPLLFNLALDDLLRLLNKEEEIKLGGPGITHLAYADDIVLFSEGKSRK---- 161
Query: 95 TMQESIDKLNHFSDQTGLYFSPQKTQCVLFSRKYKQNNIAVNLTMYDSRIEVVDQFRFLG 154
+QE + +L +S ++GL +P K++ +L K K+ +T+ + IE V+ F++LG
Sbjct: 162 -LQELLQRLQEWSKESGLKINPSKSKVMLIGNKKKRLKD---ITLNGTPIEAVETFKYLG 217
Query: 155 LTF 157
+T
Sbjct: 218 VTI 220
>gnl|CDD|187700 cd09276, Rnase_HI_RT_non_LTR, non-LTR RNase HI domain of reverse
transcriptases. Ribonuclease H (RNase H) is classified
into two families, type 1 (prokaryotic RNase HI,
eukaryotic RNase H1 and viral RNase H) and type 2
(prokaryotic RNase HII and HIII, and eukaryotic RNase
H2). Ribonuclease HI (RNase HI) is an endonuclease that
cleaves the RNA strand of an RNA/DNA hybrid in a
sequence non-specific manner. RNase H is widely present
in various organisms, including bacteria, archaea and
eukaryotes. RNase HI has also been observed as an
adjunct domain to the reverse transcriptase gene in
retroviruses, long-term repeat (LTR)-bearing
retrotransposons and non-LTR retrotransposons. RNase HI
in LTR retrotransposons perform degradation of the
original RNA template, generation of a polypurine tract
(the primer for plus-strand DNA synthesis), and final
removal of RNA primers from newly synthesized minus and
plus strands. The catalytic residues for RNase H
enzymatic activity, three aspartatic acids and one
glutamatic acid residue (DEDD), are unvaried across all
RNase H domains. The position of the RNase domain of
non-LTR and LTR transposons is at the carboxyl terminal
of the reverse transcriptase (RT) domain and their RNase
domains group together, indicating a common evolutionary
origin. Many non-LTR transposons have lost the RNase
domain because their activity is at the nucleus and
cellular RNase may suffice; however LTR retotransposons
always encode their own RNase domain because it requires
RNase activity in RNA-protein particles in the
cytoplasm. RNase H inhibitors have been explored as an
anti-HIV drug target because RNase H inactivation
inhibits reverse transcription.
Length = 128
Score = 59.6 bits (145), Expect = 6e-11
Identities = 25/68 (36%), Positives = 35/68 (51%), Gaps = 3/68 (4%)
Query: 371 IFTDGSKNDLGVGCALTIP-ERNISKRFALNKNASIFHAELLALLQSLITIKELGVN--K 427
I+TDGSK + G I + IS+ + L S+F AELLA+L++L G K
Sbjct: 2 IYTDGSKLEGRTGAGFAIVRKGTISRSYKLGPYCSVFDAELLAILEALQLALREGRRARK 61
Query: 428 ALIITDSL 435
I +DS
Sbjct: 62 ITIFSDSQ 69
>gnl|CDD|215698 pfam00078, RVT_1, Reverse transcriptase (RNA-dependent DNA
polymerase). A reverse transcriptase gene is usually
indicative of a mobile element such as a retrotransposon
or retrovirus. Reverse transcriptases occur in a variety
of mobile elements, including retrotransposons,
retroviruses, group II introns, bacterial msDNAs,
hepadnaviruses, and caulimoviruses.
Length = 194
Score = 49.3 bits (118), Expect = 8e-07
Identities = 31/142 (21%), Positives = 58/142 (40%), Gaps = 34/142 (23%)
Query: 19 KYMDERSFKIRLNNSTLSQDFSNVCGIPQGGVASSTLFAIAINTITSYI---HPSLSSSL 75
+++ R+F + +N + G+PQG V S LF + +N + + P L+
Sbjct: 84 RFIRWRTFSVLVNGN--PGGRYEWRGLPQGSVLSPLLFNLFMNELLRPLRKRFPGLTYLR 141
Query: 76 FVDDFAIFTRDKNKDLLISTMQESIDKLNHFSDQTGLYFSPQKTQCVLFSRKYKQNNIAV 135
+ DD IF++ +QE ++++ F + GL +P+KT+
Sbjct: 142 YADDILIFSKSP------EELQEILEEVLEFLKELGLKLNPEKTK--------------- 180
Query: 136 NLTMYDSRIEVVDQFRFLGLTF 157
I D+ +FLG
Sbjct: 181 --------ITHSDEVKFLGYVI 194
>gnl|CDD|187690 cd06222, RNase_H, RNase H is an endonuclease that cleaves the RNA
strand of an RNA/DNA hybrid in a sequence non-specific
manner. Ribonuclease H (RNase H) enzymes are divided
into two major families, Type 1 and Type 2, based on
amino acid sequence similarities and biochemical
properties. RNase H is an endonuclease that cleaves the
RNA strand of an RNA/DNA hybrid in a sequence
non-specific manner in the presence of divalent cations.
RNase H is widely present in various organisms,
including bacteria, archaea and eukaryotes. Most
prokaryotic and eukaryotic genomes contain multiple
RNase H genes. Despite the lack of amino acid sequence
homology, Type 1 and type 2 RNase H share a main-chain
fold and steric configurations of the four acidic
active-site residues and have the same catalytic
mechanism and functions in cells. RNase H is involved in
DNA replication, repair and transcription. One of the
important functions of RNase H is to remove Okazaki
fragments during DNA replication. RNase H inhibitors
have been explored as an anti-HIV drug target because
RNase H inactivation inhibits reverse transcription.
Length = 123
Score = 44.3 bits (105), Expect = 1e-05
Identities = 29/107 (27%), Positives = 43/107 (40%), Gaps = 14/107 (13%)
Query: 372 FTDGS--KNDLGVGCALTIPERNISKRFAL---NKNASIFHAELLALLQSLITIKELGVN 426
TDGS N G + + + FA A+ AELLALL++L +LG+
Sbjct: 1 NTDGSCKGNPGPAGAGGVLRDHEGAWLFAGSLSIPAATNNEAELLALLEALELALDLGLK 60
Query: 427 KALIITDSLMY-------PWKSSCQKSRLDEV-CLMRMRLGHSKITH 465
K +I TDS Y K + + L L+ + + H
Sbjct: 61 KLIIETDS-KYVVDLINSWSKGWKKNNLLLWDILLLLSKFIDIRFEH 106
>gnl|CDD|187697 cd09273, RNase_HI_RT_Bel, Bel/Pao family of RNase HI in long-term
repeat retroelements. Ribonuclease H (RNase H) enzymes
are divided into two major families, Type 1 and Type 2,
based on amino acid sequence similarities and
biochemical properties. RNase H is an endonuclease that
cleaves the RNA strand of an RNA/DNA hybrid in a
sequence non-specific manner in the presence of divalent
cations. RNase H is widely present in various organisms,
including bacteria, archaea and eukaryote. RNase HI has
also been observed as adjunct domains to the reverse
transcriptase gene in retroviruses, in long-term repeat
(LTR)-bearing retrotransposons and non-LTR
retrotransposons. RNase HI in LTR retrotransposons
perform degradation of the original RNA template,
generation of a polypurine tract (the primer for
plus-strand DNA synthesis), and final removal of RNA
primers from newly synthesized minus and plus strands.
The catalytic residues for RNase H enzymatic activity,
three aspartatic acids and one glutamatic acid residue
(DEDD), are unvaried across all RNase H domains.
Phylogenetic patterns of RNase HI of LTR retroelements
is classified into five major families, Ty3/Gypsy,
Ty1/Copia, Bel/Pao, DIRS1 and the vertebrate
retroviruses. Bel/Pao family has been described only in
metazoan genomes. RNase H inhibitors have been explored
as an anti-HIV drug target because RNase H inactivation
inhibits reverse transcription.
Length = 135
Score = 41.5 bits (98), Expect = 2e-04
Identities = 22/64 (34%), Positives = 31/64 (48%), Gaps = 4/64 (6%)
Query: 371 IFTDGSKNDLGVGCALTIPERNISKRFALNKNASIFHAELLALLQSLITIKELGVNKALI 430
+FTDGS G A+ ++ + L S AEL+AL+++L K VN I
Sbjct: 2 VFTDGSSFVRKAGYAVVT-GPDVLEIATLPYGTSAQRAELIALIRALELAKGKPVN---I 57
Query: 431 ITDS 434
TDS
Sbjct: 58 YTDS 61
>gnl|CDD|223405 COG0328, RnhA, Ribonuclease HI [DNA replication, recombination, and
repair].
Length = 154
Score = 39.6 bits (93), Expect = 8e-04
Identities = 24/74 (32%), Positives = 34/74 (45%), Gaps = 9/74 (12%)
Query: 367 DHVKIFTDG-SKNDLGV-GCA----LTIPERNISKRFALNKNASIFHAELLALLQSLITI 420
V+IFTDG + G G E+ +S N AEL AL+++L +
Sbjct: 2 KKVEIFTDGACLGNPGPGGWGAVLRYGDGEKELSGGEGRTTNNR---AELRALIEALEAL 58
Query: 421 KELGVNKALIITDS 434
KELG + + TDS
Sbjct: 59 KELGACEVTLYTDS 72
>gnl|CDD|215695 pfam00075, RNase_H, RNase H. RNase H digests the RNA strand of an
RNA/DNA hybrid. Important enzyme in retroviral
replication cycle, and often found as a domain
associated with reverse transcriptases. Structure is a
mixed alpha+beta fold with three a/b/a layers.
Length = 126
Score = 36.5 bits (85), Expect = 0.008
Identities = 23/71 (32%), Positives = 35/71 (49%), Gaps = 5/71 (7%)
Query: 366 KDHVKIFTDGSKN-DLGVGCALTIPERNISKRFALNKNASIFHAELLALLQSLITIKELG 424
+ V ++TDGS N + G G A + + + L + AELLAL+++L + L
Sbjct: 1 PEAVTVYTDGSCNGNPGPGGAGYVTDGGKQRSKPLP-GTTNQRAELLALIEAL---EALS 56
Query: 425 VNKALIITDSL 435
K I TDS
Sbjct: 57 GQKVNIYTDSQ 67
>gnl|CDD|205634 pfam13456, RVT_3, Reverse transcriptase-like. This domain is found
in plants and appears to be part of a retrotransposon.
Length = 88
Score = 34.9 bits (81), Expect = 0.012
Identities = 12/33 (36%), Positives = 19/33 (57%)
Query: 404 SIFHAELLALLQSLITIKELGVNKALIITDSLM 436
S AE ALL+ L ELG+ + ++ +DS +
Sbjct: 1 SPLEAEAEALLEGLQLALELGIRRLIVESDSQL 33
>gnl|CDD|187703 cd09279, RNase_HI_archaeal_like, RNAse HI family that includes
Archaeal RNase HI. Ribonuclease H (RNase H) is
classified into two evolutionarily unrelated families,
type 1 (prokaryotic RNase HI, eukaryotic RNase H1 and
viral RNase H) and type 2 (prokaryotic RNase HII and
HIII, and eukaryotic RNase H2). RNase H is an
endonuclease that cleaves the RNA strand of an RNA/DNA
hybrid in a sequence non-specific manner. RNase H is
involved in DNA replication, repair and transcription.
RNase H is widely present in various organisms,
including bacteria, archaea and eukaryotes and most
prokaryotic and eukaryotic genomes contain multiple
RNase H genes. Despite the lack of amino acid sequence
homology, Type 1 and type 2 RNase H share a main-chain
fold and steric configurations of the four acidic
active-site (DEDD) residues and have the same catalytic
mechanism and functions in cells. One of the important
functions of RNase H is to remove Okazaki fragments
during DNA replication. Most archaeal genomes contain
only type 2 RNase H (RNase HII); however, a few contain
RNase HI as well. Although archaeal RNase HI sequences
conserve the DEDD active-site motif, they lack other
common features important for catalytic function, such
as the basic protrusion region. Archaeal RNase HI
homologs are more closely related to retroviral RNase HI
than bacterial and eukaryotic type I RNase H in
enzymatic properties.
Length = 128
Score = 34.8 bits (81), Expect = 0.027
Identities = 19/71 (26%), Positives = 29/71 (40%), Gaps = 5/71 (7%)
Query: 369 VKIFTDGSKNDL----GVGCALTIPERN-ISKRFALNKNASIFHAELLALLQSLITIKEL 423
++ DG+ G G + P+ + + L A+ AE AL+ L EL
Sbjct: 1 WTLYFDGASRGNPGPAGAGIVIKSPDGEVLEQSIPLGFPATNNEAEYEALIAGLELALEL 60
Query: 424 GVNKALIITDS 434
G+ K I DS
Sbjct: 61 GIKKLEIYGDS 71
>gnl|CDD|238824 cd01646, RT_Bac_retron_I, RT_Bac_retron_I: Reverse transcriptases
(RTs) in bacterial retrotransposons or retrons. The
polymerase reaction of this enzyme leads to the
production of a unique RNA-DNA complex called msDNA
(multicopy single-stranded (ss)DNA) in which a small
ssDNA branches out from a small ssRNA molecule via a
2'-5'phosphodiester linkage. Bacterial retron RTs
produce cDNA corresponding to only a small portion of
the retron genome.
Length = 158
Score = 35.4 bits (82), Expect = 0.028
Identities = 25/108 (23%), Positives = 41/108 (37%), Gaps = 11/108 (10%)
Query: 22 DERSFKIRLNNSTLSQDFSNVCGIPQGGVASSTLFA-IAINTITSYIHPSLSSSL---FV 77
R L+ LS + G+P G + S A I +N + + L +V
Sbjct: 31 LLRLLGNLLDLLLLSSQYGQTNGLPIGPLTSR-FLANIYLNDVDHELKSKLKGVDYVRYV 89
Query: 78 DDFAIFTRDKNKDLLISTMQESIDKLNHFSDQTGLYFSPQKTQCVLFS 125
DD IF K +E +++L F + GL + KT+ +
Sbjct: 90 DDIRIFADSK------EEAEEILEELKEFLAELGLSLNLSKTEILPLP 131
>gnl|CDD|238826 cd01648, TERT, TERT: Telomerase reverse transcriptase (TERT).
Telomerase is a ribonucleoprotein (RNP) that synthesizes
telomeric DNA repeats. The telomerase RNA subunit
provides the template for synthesis of these repeats.
The catalytic subunit of RNP is known as telomerase
reverse transcriptase (TERT). The reverse transcriptase
(RT) domain is located in the C-terminal region of the
TERT polypeptide. Single amino acid substitutions in
this region lead to telomere shortening and senescence.
Telomerase is an enzyme that, in certain cells,
maintains the physical ends of chromosomes (telomeres)
during replication. In somatic cells, replication of the
lagging strand requires the continual presence of an RNA
primer approximately 200 nucleotides upstream, which is
complementary to the template strand. Since there is a
region of DNA less than 200 base pairs from the end of
the chromosome where this is not possible, the
chromosome is continually shortened. However, a surplus
of repetitive DNA at the chromosome ends protects
against the erosion of gene-encoding DNA. Telomerase is
not normally expressed in somatic cells. It has been
suggested that exogenous TERT may extend the lifespan
of, or even immortalize, the cell. However, recent
studies have shown that telomerase activity can be
induced by a number of oncogenes. Conversely, the
oncogene c-myc can be activated in human TERT
immortalized cells. Sequence comparisons place the
telomerase proteins in the RT family but reveal
hallmarks that distinguish them from retroviral and
retrotransposon relatives.
Length = 119
Score = 33.8 bits (78), Expect = 0.050
Identities = 27/99 (27%), Positives = 40/99 (40%), Gaps = 22/99 (22%)
Query: 34 TLSQDFSNVCGIPQGGVASSTLFAIAINTI----TSYIHPSLSSSL---FVDDFAIFTRD 86
++ Q + GIPQG SS L ++ + S++ SL VDDF
Sbjct: 9 SIPQYYRQKVGIPQGSPLSSLLCSLYYADLENKYLSFLDVIDKDSLLLRLVDDF------ 62
Query: 87 KNKDLLISTMQESIDK-----LNHFSDQTGLYFSPQKTQ 120
LLI+T + K L F +Q + + KTQ
Sbjct: 63 ----LLITTSLDKAIKFLNLLLRGFINQYKTFVNFDKTQ 97
>gnl|CDD|153067 cd03597, CLECT_attractin_like, C-type lectin-like domain (CTLD) of
the type found in human and mouse attractin (AtrN) and
attractin-like protein (ALP). CLECT_attractin_like:
C-type lectin-like domain (CTLD) of the type found in
human and mouse attractin (AtrN) and attractin-like
protein (ALP). CTLD refers to a domain homologous to
the carbohydrate-recognition domains (CRDs) of the
C-type lectins. Mouse AtrN (the product of the mahogany
gene) has been shown to bind Agouti protein and to
function in agouti-induced pigmentation and obesity.
Mutations in AtrN have also been shown to cause
spongiform encephalopathy and hypomyelination in rats
and hamsters. The cytoplasmic region of mouse ALP has
been shown to binds to melanocortin receptor (MCR4).
Signaling through MCR4 plays a role in appetite
suppression. Attractin may have therapeutic potential
in the treatment of obesity. Human attractin (hAtrN)
has been shown to be expressed on activated T cells and
released extracellularly. The circulating serum
attractin induces the spreading of monocytes that become
the focus of the clustering of non-proliferating T
cells.
Length = 129
Score = 32.6 bits (74), Expect = 0.18
Identities = 17/49 (34%), Positives = 25/49 (51%), Gaps = 5/49 (10%)
Query: 285 ILNPLYKPKYENSNIKPTVGIQKKNL-----EDTIPFNSIMLKALPKEP 328
+L L K + + P VG++K N+ ED PF + L+ LP EP
Sbjct: 48 VLKELQKHQMTKQKLTPWVGLRKINVSYWCWEDMSPFTNTTLQWLPGEP 96
>gnl|CDD|233302 TIGR01176, fum_red_Fp, fumarate reductase, flavoprotein subunit.
The terms succinate dehydrogenase and fumarate reductase
may be used interchangeably in certain systems. However,
a number of species have distinct complexes, with the
fumarate reductase active under anaerobic conditions.
This model represents the fumarate reductase
flavoprotein subunit from several such species in which
a distinct succinate dehydrogenase is also found. Not
all bona fide fumarate reductases will be found by this
model.
Length = 580
Score = 31.4 bits (71), Expect = 1.2
Identities = 23/81 (28%), Positives = 38/81 (46%), Gaps = 11/81 (13%)
Query: 395 KRFALNKNASIFHAELLALLQSLITIKELG--VNKALIITDSLMYPWKSSCQKSRLDEVC 452
KR ++ ++ +F+ +LL L+ ELG ++ A + S + +S RLDE C
Sbjct: 486 KRAGIDDHSRVFNTDLLYLI-------ELGGGLDVAEAMVHSALRRKESRGAHQRLDEGC 538
Query: 453 LMRMRLGHSKITHSHLFRRED 473
R + K H+ FR D
Sbjct: 539 TERDDVHFLK--HTLAFRESD 557
>gnl|CDD|222351 pfam13733, Glyco_transf_7N, N-terminal region of glycosyl
transferase group 7. This is the N-terminal half of a
family of galactosyltransferases from a wide range of
Metazoa with three related galactosyltransferases
activities, all three of which are possessed by one
sequence in some cases. EC:2.4.1.90, N-acetyllactosamine
synthase; EC:2.4.1.38,
Beta-N-acetylglucosaminyl-glycopeptide beta-1,4-
galactosyltransferase; and EC:2.4.1.22 Lactose synthase.
Note that N-acetyllactosamine synthase is a component of
Lactose synthase along with alpha-lactalbumin, in the
absence of alpha-lactalbumin EC:2.4.1.90 is the
catalyzed reaction.
Length = 136
Score = 29.0 bits (65), Expect = 2.7
Identities = 13/40 (32%), Positives = 21/40 (52%), Gaps = 1/40 (2%)
Query: 173 SCVARSRILKILSKKSWASD-RKMLIRMYKSLIRSKLDYG 211
C+ RSR I+ ++ R +L R++ L R +L YG
Sbjct: 42 GCLPRSRTAIIIPYRAREEHLRLLLYRLHPFLQRQQLAYG 81
>gnl|CDD|146200 pfam03444, HrcA_DNA-bdg, Winged helix-turn-helix transcription
repressor, HrcA DNA-binding. This domain is always
found with a pair of CBS domains pfam00571.
Length = 79
Score = 28.1 bits (63), Expect = 2.8
Identities = 8/23 (34%), Positives = 14/23 (60%)
Query: 505 STSISDILKNDEGTLKEVLQFLK 527
I+DI+ + GT++ +Q LK
Sbjct: 26 GEEIADIIGRNPGTVRNQMQSLK 48
>gnl|CDD|187702 cd09278, RNase_HI_prokaryote_like, RNase HI family found mainly in
prokaryotes. Ribonuclease H (RNase H) is classified
into two evolutionarily unrelated families, type 1
(prokaryotic RNase HI, eukaryotic RNase H1 and viral
RNase H) and type 2 (prokaryotic RNase HII and HIII, and
eukaryotic RNase H2). RNase H is an endonuclease that
cleaves the RNA strand of an RNA/DNA hybrid in a
sequence non-specific manner. RNase H is involved in DNA
replication, repair and transcription. RNase H is widely
present in various organisms, including bacteria,
archaea and eukaryotes and most prokaryotic and
eukaryotic genomes contain multiple RNase H genes.
Despite the lack of amino acid sequence homology, Type 1
and type 2 RNase H share a main-chain fold and steric
configurations of the four acidic active-site (DEDD),
residues and have the same catalytic mechanism and
functions in cells. One of the important functions of
RNase H is to remove Okazaki fragments during DNA
replication. Prokaryotic RNase H varies greatly in
domain structures and substrate specificities.
Prokaryotes and some single-cell eukaryotes do not
require RNase H for viability.
Length = 139
Score = 28.6 bits (65), Expect = 3.7
Identities = 18/74 (24%), Positives = 30/74 (40%), Gaps = 15/74 (20%)
Query: 369 VKIFTDGS---KNDLGVGCALTIPERNISKRFALNKNASIFHA-----ELLALLQSLITI 420
+ I+TDG+ G G A + + K + EL A++++L +
Sbjct: 2 ITIYTDGACLGNPGPG-GWAAILRYGDHEKELS----GGEAGTTNNRMELTAVIEALEAL 56
Query: 421 KELGVNKALIITDS 434
KE L+ TDS
Sbjct: 57 KEPC--PVLLYTDS 68
>gnl|CDD|238134 cd00217, INT_Flp, Flp recombinase, C-terminal catalytic domain.
Yeast Flp-like recombinases mediate the amplification of
the 2 micron circular plasmid copy number by catalyzing
the intra-molecular recombination between two inverted
repeats during replication. They belong to the DNA
breaking-rejoining enzyme superfamily, which also
includes prokaryotic tyrosine recombinases and type IB
topoisomerases. These enzymes share the same fold in
their catalytic domain containing six conserved active
site residues and the overall reaction mechanism.
Flp-like recombinases are almost exclusively found in
yeast and are highly diverged in sequence from the
prokaryotic tyrosine recombinases. They cleave their
target DNA in trans with a composite active site in
which the catalytic tyrosine is provided by a promoter
bound to a site other than the one being cleaved. Thus
each active site within Flp complexes is assembled by
domain swapping and contains catalytic residues from two
different monomers. Two DNA segments are synapsed by the
tetrameric enzyme, carrying the nucleophilic tyrosine in
each active site with only two of the four monomers
active at a given time. The catalytic domain is linked
through a flexible loop to the N-terminal domain, which
is largely responsible for non-specific DNA binding and
isomerization. Its overall fold is similar to the SAM
domain fold also found in the N-terminal domains of
lambda integrase and XerD recombinase.
Length = 339
Score = 29.7 bits (67), Expect = 3.9
Identities = 15/61 (24%), Positives = 23/61 (37%)
Query: 164 KIHLRNLKQSCVARSRILKILSKKSWASDRKMLIRMYKSLIRSKLDYGCPAYNSASANTL 223
+ ++ L Q + I + + AS MLI M + R P Y S + TL
Sbjct: 3 ETPIKVLIQDILETLTIGSNQTGEKLASLLTMLILMANAAGREIKINTFPKYKSCISKTL 62
Query: 224 Q 224
Sbjct: 63 S 63
>gnl|CDD|173953 cd08194, Fe-ADH6, Iron-containing alcohol dehydrogenases-like.
Iron-containing alcohol dehydrogenase-like. Proteins of
this family have not been characterized. Their specific
function is unknown. The protein structure represents a
dehydroquinate synthase-like fold and belongs to the
alcohol dehydrogenase-like superfamily. They are
distinct from other alcohol dehydrogenases which contain
different protein domains. Alcohol dehydrogenase
catalyzes the reduction of acetaldehyde to alcohol with
NADP as cofactor. Its activity requires iron ions.
Length = 375
Score = 29.9 bits (68), Expect = 3.9
Identities = 8/25 (32%), Positives = 16/25 (64%)
Query: 412 ALLQSLITIKELGVNKALIITDSLM 436
A+ ++ + +LG + LI+TD +M
Sbjct: 10 AVDETGAVLADLGGKRPLIVTDKVM 34
>gnl|CDD|225243 COG2368, COG2368, Aromatic ring hydroxylase [Secondary metabolites
biosynthesis, transport, and catabolism].
Length = 493
Score = 29.6 bits (67), Expect = 5.1
Identities = 17/68 (25%), Positives = 28/68 (41%), Gaps = 6/68 (8%)
Query: 329 WLLKSPKYDLSLSTYKKESMPAQFFQNEFKNKIEENFKDHVKIFTDGSKNDLGVGCALTI 388
+ + P YD + + F EN +++ K KNDL + A+T
Sbjct: 100 CMGRCPDYD---ALNAMAFGSGAEAEPGFGTDYHENAREYYKEVQ---KNDLALTHAITD 153
Query: 389 PERNISKR 396
P+ + SKR
Sbjct: 154 PKGDRSKR 161
>gnl|CDD|149028 pfam07737, ATLF, Anthrax toxin lethal factor, N- and C-terminal
domain. The C-terminal domain is the catalytically
active domain whereas the N-terminal domain is likely to
be inactive.
Length = 226
Score = 29.1 bits (65), Expect = 5.2
Identities = 16/82 (19%), Positives = 35/82 (42%), Gaps = 5/82 (6%)
Query: 60 INTITSYIHPSLSS-SLFVDDFAIFTRD---KNKDLLISTMQESIDKLNHFSDQTGLYFS 115
I T Y + S ++ + + D K K+L + ++ I+++NH D Y
Sbjct: 96 IYTHEDYAYNQEHSKEVYYEIGKSISLDIPSKGKELR-NPSEKFINEINHAVDDYAGYLL 154
Query: 116 PQKTQCVLFSRKYKQNNIAVNL 137
+LF +K++ +++
Sbjct: 155 DSDGSDLLFIDIFKEHGSNLDV 176
>gnl|CDD|99852 cd06149, ISG20, DEDDh 3'-5' exonuclease domain of Interferon
Stimulated Gene product of 20 kDa, and similar proteins.
Interferon (IFN) Stimulated Gene product of 20 kDa
(ISG20) is an IFN-induced antiviral exonuclease with a
strong preference for single-stranded RNA and minor
activity towards single-stranded DNA. It was also
independently identified by its response to estrogen and
was called HEM45 (human estrogen regulated transcript).
ISG20 is a DEDDh-type DnaQ-like 3'-5' exonuclease
containing three conserved sequence motifs termed ExoI,
ExoII and ExoIII with a specific Hx(4)D conserved
pattern at ExoIII. These motifs are clustered around the
active site and contain four conserved acidic residues
that serve as ligands for the two metal ions required
for catalysis. ISG20 may be a major effector of innate
immunity against pathogens including viruses, bacteria,
and parasites. It is located in promyelocytic leukemia
(PML) nuclear bodies, sites for oncogenic DNA viral
transcription and replication. It may carry out its
function by degrading viral RNAs as part of the
IFN-regulated antiviral response.
Length = 157
Score = 28.6 bits (64), Expect = 5.5
Identities = 18/54 (33%), Positives = 24/54 (44%), Gaps = 12/54 (22%)
Query: 139 MYDSRI----EVVD-QFRFLGLTFDKKMNWKIHLRNLKQSCVARSRILKILSKK 187
+YD I V D + R+ G+ + HL N VA+ ILKIL K
Sbjct: 32 LYDKYIRPEGPVTDYRTRWSGIR-------RQHLVNATPFAVAQKEILKILKGK 78
>gnl|CDD|238414 cd00799, INT_Cre, Cre recombinase, C-terminal catalytic domain.
Cre-like recombinases belong to the superfamily of DNA
breaking-rejoining enzymes, which share the same fold in
their catalytic domain and the overall reaction
mechanism. The bacteriophage P1 Cre recombinase
maintains the circular phage replicon in a monomeric
state by catalyzing a site-specific recombination
between two loxP sites. The catalytic core domain of
Cre recombinase is linked to a more divergent helical
N-terminal domain, which interacts primarily with the
DNA major groove proximal to the crossover region.
Length = 287
Score = 28.5 bits (64), Expect = 8.9
Identities = 9/24 (37%), Positives = 12/24 (50%)
Query: 451 VCLMRMRLGHSKITHSHLFRREDR 474
V + L ++I LFRR DR
Sbjct: 179 VRALERWLEAARIPKGPLFRRIDR 202
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 0.135 0.395
Gapped
Lambda K H
0.267 0.0647 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 26,467,612
Number of extensions: 2533999
Number of successful extensions: 2119
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2108
Number of HSP's successfully gapped: 38
Length of query: 535
Length of database: 10,937,602
Length adjustment: 102
Effective length of query: 433
Effective length of database: 6,413,494
Effective search space: 2777042902
Effective search space used: 2777042902
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: 61 (27.4 bits)