RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12152
(133 letters)
>gnl|CDD|198402 cd10455, GIY-YIG_SLX1, Catalytic GIY-YIG domain of yeast
structure-specific endonuclease subunit SLX1 and its
eukaryotic homologs. Structure-specific endonuclease
subunit SLX1 is a highly conserved protein from yeast
to human, with an N-terminal GIY-YIG endonuclease
domain and a C-terminal PHD-type zinc finger postulated
to mediate protein-protein or protein-DNA interaction.
SLX1 forms active heterodimeric complexes with its SLX4
partner, which has additional roles in the DNA damage
response that are distinct from the function of the
heterodimeric SLX1-SLX4 nuclease. In yeast, the
SLX1-SLX4 complex functions as a 5' flap endonuclease
that maintains ribosomal DNA copy number, where SLX1
and SLX4 are shown to be catalytic and regulatory
subunits, respectively. This endonuclease introduces
single-strand cuts in duplex DNA on the 3' side of
junctions with single-strand DNA. In addition to 5'
flap endonuclease activity, human SLX1-SLX4 complex has
been identified as a Holliday junction resolvase that
promotes symmetrical cleavage of static and migrating
Holliday junctions. SLX1 also associates with MUS81,
EME1, C20orf94, PLK1, and ERCC1. Some eukaryotic SLX1
homologs lack the zinc finger domain, but possess
intrinsically unstructured extensions of unknown
function. These unstructured segments might be involved
in interactions with other proteins.
Length = 76
Score = 143 bits (363), Expect = 5e-46
Identities = 51/76 (67%), Positives = 65/76 (85%), Gaps = 1/76 (1%)
Query: 3 FHGVYLLYSRNPRYLGRTYIGYTVDPDRRIKQHNKGKDFGGAHKTSNRGPWDMVLIVYGF 62
F+GVYLL S NP+Y GRTYIG+TV+P RR++QHN G+ GGA KTS + PW+MVLIV+GF
Sbjct: 1 FYGVYLLRSLNPKYKGRTYIGFTVNPPRRLRQHN-GELKGGAKKTSRKRPWEMVLIVHGF 59
Query: 63 PNDISALRFEWAWQHP 78
P+ ++AL+FEWAWQHP
Sbjct: 60 PSKVAALQFEWAWQHP 75
>gnl|CDD|198396 cd10449, GIY-YIG_SLX1_like, Catalytic GIY-YIG domain of yeast
structure-specific endonuclease subunit SLX1 and its
homologs. Structure-specific endonuclease subunit SLX1
is a highly conserved protein from yeast to human, with
an N-terminal GIY-YIG endonuclease domain and a
C-terminal PHD-type zinc finger postulated to mediate
protein-protein or protein-DNA interaction. SLX1 forms
active heterodimeric complexes with its SLX4 partner,
which has additional roles in the DNA damage response
that are distinct from the function of the
heterodimeric SLX1-SLX4 nuclease. In yeast, the
SLX1-SLX4 complex functions as a 5' flap endonuclease
that maintains ribosomal DNA copy number, where SLX1
and SLX4 are shown to be catalytic and regulatory
subunits, respectively. This endonuclease introduces
single-strand cuts in duplex DNA on the 3' side of
junctions with single-strand DNA. In addition to 5'
flap endonuclease activity, human SLX1-SLX4 complex has
been identified as a Holliday junction resolvase that
promotes symmetrical cleavage of static and migrating
Holliday junctions. SLX1 also associates with MUS81,
EME1, C20orf94, PLK1, and ERCC1. Some eukaryotic SLX1
homologs lack the zinc finger domain, but possess
intrinsically unstructured extensions of unknown
function. These unstructured segments might be involved
in interactions with other proteins.
Length = 67
Score = 71.1 bits (175), Expect = 1e-17
Identities = 30/74 (40%), Positives = 40/74 (54%), Gaps = 8/74 (10%)
Query: 6 VYLLYSRNPRYLGRTYIGYTVDPDRRIKQHNKGKDFGGAHKTSNRGPWDMVLIVYGFPND 65
VY+LYS L R YIGYT D +RR++QHN GK + TS PW++V F +
Sbjct: 2 VYILYSE---KLDRYYIGYTSDLERRLEQHNSGK----SKFTSKYRPWELVYSEA-FESK 53
Query: 66 ISALRFEWAWQHPK 79
AL+ E + K
Sbjct: 54 SEALKREKYLKSGK 67
>gnl|CDD|216559 pfam01541, GIY-YIG, GIY-YIG catalytic domain. This domain called
GIY-YIG is found in the amino terminal region of
excinuclease abc subunit c (uvrC), bacteriophage T4
endonucleases segA, segB, segC, segD and segE; it is
also found in putative endonucleases encoded by group I
introns of fungi and phage. The structure of I-TevI a
GIY-YIG endonuclease, reveals a novel alpha/beta-fold
with a central three-stranded antiparallel beta-sheet
flanked by three helices. The most conserved and
putative catalytic residues are located on a shallow,
concave surface and include a metal coordination site.
Length = 76
Score = 50.8 bits (122), Expect = 1e-09
Identities = 20/74 (27%), Positives = 30/74 (40%), Gaps = 9/74 (12%)
Query: 3 FHGVYLLYSRNPRYLGRTYIGYTVDPDRRIKQHNKGKDFGGAHKTSNRGPWDMVLIVYGF 62
GVY++ +++ + L Y+G T + RR+KQH GK R LI+
Sbjct: 1 KPGVYIITNKDNKVL---YVGSTKNLKRRLKQHFSGKG-----AKKTRNKKPFELIILEE 52
Query: 63 PNDIS-ALRFEWAW 75
AL E
Sbjct: 53 FPTKEEALELEKYL 66
>gnl|CDD|198403 cd10456, GIY-YIG_UPF0213, The GIY-YIG domain of uncharacterized
protein family UPF0213 related to structure-specific
endonuclease SLX1. This family contains a group of
uncharacterized proteins found mainly in bacteria and
several in dsDNA viruses. Although their function roles
have not been recognized, these proteins show
significant sequence similarities with the N-terminal
GIY-YIG endonuclease domain of structure-specific
endonuclease subunit SLX1, which binds another
structure-specific endonuclease subunit SLX4 to form an
active heterodimeric SLX1-SLX4 complex. This complex
functions as a 5' flap endonuclease in yeast, and has
also been identified as a Holliday junction resolvase
in human.
Length = 68
Score = 49.3 bits (119), Expect = 3e-09
Identities = 26/71 (36%), Positives = 35/71 (49%), Gaps = 12/71 (16%)
Query: 6 VYLLYSRNPRYLGRTYIGYTVDPDRRIKQHNKGKDFGGAHKTSNRGPWDMVLIVY--GFP 63
VY+L + G Y G T D +RR+ +HN GK GA T R P V +VY F
Sbjct: 3 VYILRCAD----GSLYTGITTDLERRLAEHNSGK---GAKYTRGRRP---VKLVYSEEFD 52
Query: 64 NDISALRFEWA 74
+ AL+ E+
Sbjct: 53 DRSEALKREYR 63
>gnl|CDD|225383 COG2827, COG2827, Predicted endonuclease containing a URI domain
[DNA replication, recombination, and repair].
Length = 95
Score = 46.6 bits (111), Expect = 8e-08
Identities = 25/71 (35%), Positives = 32/71 (45%), Gaps = 8/71 (11%)
Query: 4 HGVYLLYSRNPRYLGRTYIGYTVDPDRRIKQHNKGKDFGGAHKTSNRGPWDMVLIVYGFP 63
VY+L + G Y G T D +RR+ +HN GK GA T GP +V F
Sbjct: 5 WYVYILRCAD----GTLYTGVTTDLERRLAEHNSGK---GAKYTRRYGPVRLV-WYEEFD 56
Query: 64 NDISALRFEWA 74
+ ALR E
Sbjct: 57 DKSEALRREKR 67
>gnl|CDD|178979 PRK00329, PRK00329, GIY-YIG nuclease superfamily protein;
Validated.
Length = 86
Score = 46.1 bits (110), Expect = 1e-07
Identities = 27/88 (30%), Positives = 39/88 (44%), Gaps = 10/88 (11%)
Query: 4 HGVYLLYSRNPRYLGRTYIGYTVDPDRRIKQHNKGKDFGGAHKTSNRGPWDMVLI-VYGF 62
+YLL + G Y G T D +RR QH GK GA T R P + L+ V
Sbjct: 7 WFLYLLRCAD----GSLYTGITTDVERRFAQHQSGK---GAKYTRGRPP--LTLVFVEPV 57
Query: 63 PNDISALRFEWAWQHPKMSRRLQHVARK 90
+ ALR E+ ++ ++ + VA
Sbjct: 58 GDRSEALRAEYRFKQLTKKQKERLVAEG 85
>gnl|CDD|214677 smart00465, GIYc, GIY-YIG type nucleases (URI domain).
Length = 84
Score = 45.1 bits (107), Expect = 2e-07
Identities = 16/71 (22%), Positives = 26/71 (36%), Gaps = 10/71 (14%)
Query: 4 HGVYLLYSRNPRYLGRTYIGYTVDPDRRIKQHNKGKDFGGAHKTSNRGPWDMVLIVYGFP 63
GVY + ++ L Y+G + R+K+H G R D +L G
Sbjct: 2 PGVYYITNKKNGKL---YVGKAKNLRNRLKRHFSGSR-------KGRLLIDALLKYGGNF 51
Query: 64 NDISALRFEWA 74
I F+ +
Sbjct: 52 EFIILESFDES 62
>gnl|CDD|198394 cd10447, GIY-YIG_unchar_2, GIY-YIG domain of uncharacterized
hypothetical protein found in bacteria and archaea.
The family includes a group of uncharacterized
hypothetical proteins, mainly found in bacteria and a
few found in archaea, with a GIY-YIG domain that shows
statistically significant similarity to the N-terminal
catalytic domains of GIY-YIG family of intron-encoded
homing endonuclease I-TevI and catalytic GIY-YIG domain
of nucleotide excision repair endonuclease UvrC.
Length = 80
Score = 36.4 bits (85), Expect = 4e-04
Identities = 15/38 (39%), Positives = 20/38 (52%), Gaps = 1/38 (2%)
Query: 5 GVYLLYSRNP-RYLGRTYIGYTVDPDRRIKQHNKGKDF 41
GVY L+ + YIG + +R+KQH K KDF
Sbjct: 1 GVYFLFGEDDEGGKPTVYIGEAENVLKRLKQHLKDKDF 38
>gnl|CDD|198380 cd00719, GIY-YIG_SF, GIY-YIG nuclease domain superfamily. The
GIY-YIG nuclease domain superfamily includes a large
and diverse group of proteins involved in many cellular
processes, such as class I homing GIY-YIG family
endonucleases, prokaryotic nucleotide excision repair
proteins UvrC and Cho, type II restriction enzymes, the
endonuclease/reverse transcriptase of eukaryotic
retrotransposable elements, and a family of eukaryotic
enzymes that repair stalled replication forks. All of
these members contain a conserved GIY-YIG nuclease
domain that may serve as a scaffold for the
coordination of a divalent metal ion required for
catalysis of the phosphodiester bond cleavage. By
combining with different specificity, targeting, or
other domains, the GIY-YIG nucleases may perform
different functions.
Length = 69
Score = 36.2 bits (84), Expect = 5e-04
Identities = 16/72 (22%), Positives = 27/72 (37%), Gaps = 9/72 (12%)
Query: 5 GVYLLYSRNPRYLGRTYIGYTVDPDRRIKQHNKGKDFGGAHKTSNRGPWDMVLIVYGFPN 64
GVY+LY + + Y+G T + RIK+H + + +G ++
Sbjct: 1 GVYVLYDEDNGLI---YVGQTKNLRNRIKEHLRKQRSD-----WTKGLKPFEILYLEVAP 52
Query: 65 -DISALRFEWAW 75
S L A
Sbjct: 53 EAESELLDLEAA 64
>gnl|CDD|220802 pfam10544, T5orf172, T5orf172 domain. This domain was identified
by Iyer and colleagues.
Length = 90
Score = 33.5 bits (77), Expect = 0.006
Identities = 15/59 (25%), Positives = 26/59 (44%), Gaps = 10/59 (16%)
Query: 6 VYLLYSRNPRYLGRTYIGYTVDPDRRIKQHNKGKDFGGAHKTSNRGPWDMVLIVYGFPN 64
VY++ NP G IG T + +RR+K+ N T + +++V I +
Sbjct: 3 VYVI--TNPSNKGLYKIGRTTNLERRLKELNSS--------TGSPDEFEVVYIEVINED 51
>gnl|CDD|222142 pfam13455, MUG113, Meiotically up-regulated gene 113. This is a
family of fungal proteins found to be up-regulated in
meiosis.
Length = 76
Score = 30.7 bits (70), Expect = 0.043
Identities = 13/51 (25%), Positives = 25/51 (49%), Gaps = 13/51 (25%)
Query: 22 IGYTVDPDRRIKQHNKGKDFGGAHKTSNRGPWDMVLIVYGFPNDISALRFE 72
IG T + +RR+K+ +K P+D ++ Y +P+ +A + E
Sbjct: 3 IGRTTNLERRLKELSKQ------------CPFDFEVVAY-YPSVPNARKLE 40
>gnl|CDD|198386 cd10439, GIY-YIG_COG3410, GIY-YIG domain of uncharacterized
bacterial protein structurally related to COG3410.
This family contains a group of uncharacterized
bacterial proteins. Although their function roles have
not been recognized, these proteins contain a putative
GIY-YIG domain in their N-terminus. Moreover, a
conserved domain COG3410 with unknown function has been
found in the C-terminus of most family members.
Length = 80
Score = 29.5 bits (67), Expect = 0.16
Identities = 14/41 (34%), Positives = 21/41 (51%), Gaps = 3/41 (7%)
Query: 6 VYLLYSRNPRYLGRTYIGYTVDPDRRIKQHNKGKDFGGAHK 46
VY+LY + + + YIG T + RR+KQH K +
Sbjct: 5 VYILYDKKKK---KVYIGETNNILRRLKQHLKDPEKKFLRD 42
>gnl|CDD|129823 TIGR00740, TIGR00740, tRNA (cmo5U34)-methyltransferase. This tRNA
methyltransferase is involved, together with cmoB, in
preparing the uridine-5-oxyacetic acid (cmo5U) at
position 34 [Unknown function, Enzymes of unknown
specificity].
Length = 239
Score = 29.5 bits (66), Expect = 0.38
Identities = 16/54 (29%), Positives = 26/54 (48%)
Query: 78 PKMSRRLQHVARKKSKETTYTYCLRLLHIMLQTAPWQRLPLTVQWLKPEYQQVL 131
P + R QH+A S+ C + H+ ++ A L T+Q+L PE + L
Sbjct: 90 PMVERCRQHIAAYHSEIPVEILCNDIRHVEIKNASMVILNFTLQFLPPEDRIAL 143
>gnl|CDD|198395 cd10448, GIY-YIG_unchar_3, GIY-YIG domain of uncharacterized
hypothetical protein found in bacteria. The family
includes a group of uncharacterized bacterial proteins
with a GIY-YIG domain that shows statistically
significant similarity to the N-terminal catalytic
domains of GIY-YIG family of intron-encoded homing
endonuclease I-TevI and catalytic GIY-YIG domain of
nucleotide excision repair endonuclease UvrC.
Length = 87
Score = 28.2 bits (64), Expect = 0.51
Identities = 14/34 (41%), Positives = 19/34 (55%), Gaps = 3/34 (8%)
Query: 6 VYLLYSRNPRYLGRTYIGYTVDPDRRIKQHNKGK 39
VY+L ++ G YIG T D RRI +H +G
Sbjct: 3 VYILANKRN---GTLYIGVTSDLIRRIYEHKEGL 33
>gnl|CDD|198384 cd10437, GIY-YIG_HE_I-TevI_like, N-terminal catalytic domain of
GIY-YIG intron endonuclease I-TevI, I-BmoI, I-BanI,
I-BthII and similar proteins. I-TevI is a
site-specific GIY-YIG homing endonuclease encoded
within the group I intron of the thymidylate synthase
gene (td) from Escherichia coli phage T4. It functions
as an endonuclease that catalyzes the first step in
intron homing by generating a double-strand break in
the intronless td allele within a sequence designated
the homing site. I-TevI recognizes its extensive 37
base pair DNA target in a site-specific, but
sequence-tolerant manner. The cleavage site is located
at 23 (upper strand) and 25 (lower strand) nucleotides
upstream of the intron insertion site. A divalent
cation, such as Mg2+, is required for the catalysis.
I-TevI also acts as a repressor of its own
transcription. It binds an operator that is located
upstream of the I-TevI coding sequence and overlaps the
T4 late promoter, which drives I-TevI expression from
within the td intron. I-TevI binds the homing sites and
the operator with the same affinity, but cleaves the
homing site more efficiently than the operator. I-TevI
consists of an N-terminal catalytic domain, containing
the GIY-YIG motif, and a C-terminal DNA-binding domain
that binds DNA as a monomer, joined by a flexible
linker. The C-terminal domain includes three
subdomains: a zinc finger, a minor-groove binding
alpha-helix (NUMOD3, nuclease-associated modular domain
3), and a helix-turn-helix domain (HTH). The last two
are responsible for DNA-binding. The zinc finger is
part of the linker and not required for DNA-binding. It
is implicated as a distance sensor to constrain the
catalytic domain to cleave the homing site at a fixed
position. None of other GIY-YIG endonucleases have been
found to have the zinc finger motif. This family also
includes a reduced activity isoschizomer of I-TevI,
I-BmoI, which is encoded within the group I intron of
the thymidylate synthase (TS) gene (thyA) from Bacillus
mojavensis. I-BmoI catalyzes the first step in intron
homing by generating a double-strand break in the
intronless td allele within a sequence designated the
homing site in the presence of a divalent cation
cofactor, such as Mg2+. In the absence of Mg2+, I-Bmol
only nicks one of the strands. Both I-BmoI and I-TevI
bind a homologous stretch of TS-encoding DNA as
monomers, but use different strategies to distinguish
intronless from intron-containing substrates. I-TevI
recognizes substrates at the level of DNA-binding.
However, I-BmoI binds both intron-containing and
intronless TS-encoding substrates, but efficiently
cleaves only intronless substrate. Afterwards they
cleave their respective intronless substrates in the
same positions, and both require a critical G-C base
pair adjacent to the top strand site for efficient
cleavage. The C-terminal domain of I-BmoI has
nuclease-associated modular DNA-binding domains
(NUMODs), but lacks the zinc finger, which is different
from that of I-TevI. Although the zinc finger
implicated as a distance determination in I-TevI is
absent, I-BmoI still possesses some cleavage distance
discrimination. Besides I-TevI and I-BmoI, this family
contains a putative GIY-YIG homing endonuclease,
I-BanI, encoded within the self-splicing group I intron
of nrdE gene from Bacillus anthracis. It contains two
major domains, the N-terminal GIY-YIG domain and the
C-terminal DNA-binding domain that consists of a
minor-groove DNA binding alpha-helix motif and a
helix-turn-helix (HTH) motif. I-BanI generates a
double-strand break (DSB) in the intronless nrdE gene.
The cleavage site is located at 5 and 7 nucleotides
upstream of the intron insertion site, with
2-nucleotide 3' extensions. The recognition site is 35
to 40 base pairs and covers the cleavage site with a
bias toward the downstream region including the
(intervening sequence) IVS insertion site. Moreover,
this family contains another putative GIY-YIG homing
endonuclease, I-BthII, encoded within the self-splicing
group I intron of nrdF gene from Bacillus thuringiensis
ssp. pakistani. It contains a GIY-YIG motif that
generates a double-strand break (DSB) in the intronless
nrdF gene. The cleavage site is located at 7 and 9
nucleotides upstream of the intron insertion site,
leaving 2-nucleotide 3' extensions. The recognition
site is 27 to 29 base pairs with the DSB cleavage site
at the 5'-end of the top strand, and with the
intervening sequence (IVS) insertion site approximately
in the middle of the recognition site.
Length = 90
Score = 27.2 bits (61), Expect = 1.4
Identities = 9/32 (28%), Positives = 17/32 (53%), Gaps = 3/32 (9%)
Query: 4 HGVYLLYSRNPRYLGRTYIGYTVDPDRRIKQH 35
G+Y + + G+ YIG + + +R+ QH
Sbjct: 1 SGIYKITNLE---NGKIYIGSSKNILKRLSQH 29
>gnl|CDD|222942 PHA02924, PHA02924, hypothetical protein; Provisional.
Length = 156
Score = 26.6 bits (58), Expect = 3.4
Identities = 14/39 (35%), Positives = 20/39 (51%), Gaps = 6/39 (15%)
Query: 59 VYGFPNDISALRFEWAWQHPKMSRRLQHVARKKSKETTY 97
+Y DI+A+ F+ R LQ++A KK K T Y
Sbjct: 60 IYDLAKDINAMSFD------SFIRSLQNIASKKDKLTVY 92
>gnl|CDD|200413 TIGR04162, exo_VPEID, exosortase E/protease, VPEID-CTERM system.
Members of this protein family are fusion proteins of
exosortase (N-terminal) and a CAAX prenyl protease
domain (C-terminal). Members are restricted to the alpha
Proteobacteria. The variant C-terminal protein sequence
VPEID-CTERM occurs only in these species, often
adjacent.
Length = 519
Score = 27.1 bits (60), Expect = 3.6
Identities = 15/57 (26%), Positives = 22/57 (38%), Gaps = 2/57 (3%)
Query: 75 WQHPKMSRRLQHVARKKSKETTYTYCLRLLHIMLQTAPWQRLPLTVQWLKPEYQQVL 131
W P + L H+A L + ++L P RLPL L ++ Q L
Sbjct: 56 WARPNLWHALAHLAASAPGRRLRWAALHVAGLVLILVPLARLPLAQ--LNAQFSQAL 110
>gnl|CDD|221734 pfam12722, Hid1, High-temperature-induced dauer-formation protein.
Hid1 (high-temperature-induced dauer-formation protein
1) represents proteins of approximately 800 residues
long and is conserved from fungi to humans. It contains
up to seven potential transmembrane domains separated by
regions of low complexity. Functionally it might be
involved in vesicle secretion or be an inter-cellular
signalling protein or be a novel insulin receptor.
Length = 813
Score = 26.6 bits (59), Expect = 4.7
Identities = 9/24 (37%), Positives = 13/24 (54%)
Query: 85 QHVARKKSKETTYTYCLRLLHIML 108
+ K S+E Y L+LL +ML
Sbjct: 278 NNSVFKDSREILVEYSLQLLLVML 301
>gnl|CDD|181575 PRK08883, PRK08883, ribulose-phosphate 3-epimerase; Provisional.
Length = 220
Score = 26.5 bits (58), Expect = 5.0
Identities = 10/27 (37%), Positives = 19/27 (70%)
Query: 8 LLYSRNPRYLGRTYIGYTVDPDRRIKQ 34
LL S NP + G+++I +T+D R +++
Sbjct: 133 LLMSVNPGFGGQSFIPHTLDKLRAVRK 159
>gnl|CDD|233421 TIGR01453, grpIintron_endo, group I intron endonuclease. This
model represents one subfamily of endonucleases
containing the endo/excinuclease amino terminal domain,
pfam01541 at its amino end. A distinct subfamily
includes excinuclease abc subunit c (uvrC). Members of
pfam01541 are often termed GIY-YIG endonucleases after
conserved motifs near the amino end. This subfamily in
This model is found in open reading frames of group I
introns in both phage and mitochondria. The closely
related endonucleases of phage T4: segA, segB, segC,
segD and segE, score below the trusted cutoff for the
family.
Length = 214
Score = 26.2 bits (58), Expect = 5.4
Identities = 17/60 (28%), Positives = 29/60 (48%), Gaps = 9/60 (15%)
Query: 5 GVYLLYSRNPRYLGRTYIGYTVDPDRRIKQHNKGKDFGGAHKTSNRGPWDMVLIVYGFPN 64
G+Y + + G+ Y+G +V+ ++R+K+H K K NR L YG+ N
Sbjct: 3 GIYKITNNI---NGKIYVGSSVNLEKRLKEHLK------LLKKGNRIKLQKALNKYGWSN 53
>gnl|CDD|233451 TIGR01531, glyc_debranch, glycogen debranching enzymye. glycogen
debranching enzyme possesses two different catalytic
activities; oligo-1,4-->1,4-glucantransferase (EC
2.4.1.25) and amylo-1,6-glucosidase (EC 3.2.1.33). Site
directed mutagenesis studies in S. cerevisiae indicate
that the transferase and glucosidase activities are
independent and located in different regions of the
polypeptide chain. Proteins in this model belong to the
larger alpha-amylase family. The model covers eukaryotic
proteins with a seed composed of human, nematode and
yeast sequences. Yeast seed sequence is well
characterized. The model is quite rigorous; either query
sequence yields large bit score or it fails to hit the
model altogether. There doesn't appear to be any middle
ground [Energy metabolism, Biosynthesis and degradation
of polysaccharides].
Length = 1464
Score = 26.3 bits (58), Expect = 7.4
Identities = 14/52 (26%), Positives = 20/52 (38%), Gaps = 6/52 (11%)
Query: 72 EWAWQHPKMSRRLQHVARKKSKETT------YTYCLRLLHIMLQTAPWQRLP 117
EW W R H K +Y L+ L+ L+ +PW+ LP
Sbjct: 1382 EWVWPIGYFLRARLHFHFKTGPRCQAAAIKPVSYLLQQLYYHLKESPWRGLP 1433
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
0.324 0.139 0.460
Gapped
Lambda K H
0.267 0.0675 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,988,255
Number of extensions: 591667
Number of successful extensions: 613
Number of sequences better than 10.0: 1
Number of HSP's gapped: 609
Number of HSP's successfully gapped: 32
Length of query: 133
Length of database: 10,937,602
Length adjustment: 86
Effective length of query: 47
Effective length of database: 7,123,158
Effective search space: 334788426
Effective search space used: 334788426
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 53 (24.3 bits)