RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15550
(125 letters)
>gnl|CDD|211399 cd11561, W2_eIF5, C-terminal W2 domain of eukaryotic translation
initiation factor 5. eIF5 functions as a GTPase
acceleration protein (GAP), as well as a GDP
dissociation inhibitor (GDI) during translational
initiation in eukaryotes. The structure of this
C-terminal domain resembles that of a set of
concatenated HEAT repeats.
Length = 157
Score = 117 bits (296), Expect = 5e-35
Identities = 49/89 (55%), Positives = 63/89 (70%), Gaps = 1/89 (1%)
Query: 6 RFTHEDIKAQRYLLNGIEQVIALHKEKLLSMVPGILKLFYDYDILEEKVLLEWAEKTSKK 65
+ ++ KAQ+ LL GIE+ H +LL VP ILK YD DILEE+V+L+W EK SKK
Sbjct: 70 KLVTDE-KAQKALLGGIERFCGKHSPELLKKVPLILKALYDNDILEEEVILKWYEKVSKK 128
Query: 66 YVSKELSAEIRSRAEPFIKWLREAEEEDS 94
YVSKE S ++R AEPF++WL EAEEE+
Sbjct: 129 YVSKEKSKKVRKAAEPFVEWLEEAEEEEE 157
>gnl|CDD|216850 pfam02020, W2, eIF4-gamma/eIF5/eIF2-epsilon. This domain of
unknown function is found at the C-terminus of several
translation initiation factors.
Length = 75
Score = 80.4 bits (199), Expect = 2e-21
Identities = 34/77 (44%), Positives = 50/77 (64%), Gaps = 2/77 (2%)
Query: 13 KAQRYLLNGIEQVIALHKEKLLSMVPGILKLFYDYDILEEKVLLEWAEKTSKKYVSKELS 72
AQ+ LL +E+ +L+ ++P ILKL YD DILEE+ +L+W EK+ K V E S
Sbjct: 1 DAQKDLLGALERFCGKENPELIKLLPKILKLLYDLDILEEEAILKWYEKSKK--VDGEGS 58
Query: 73 AEIRSRAEPFIKWLREA 89
++R +A+PF+ WL EA
Sbjct: 59 KKVRKQAKPFVTWLEEA 75
>gnl|CDD|214705 smart00515, eIF5C, Domain at the C-termini of GCD6, eIF-2B
epsilon, eIF-4 gamma and eIF-5.
Length = 83
Score = 70.4 bits (173), Expect = 3e-17
Identities = 36/84 (42%), Positives = 50/84 (59%), Gaps = 5/84 (5%)
Query: 6 RFTHEDIKAQRYLLNGIEQVIALHKEKLLSMVPGILKLFYDYDILEEKVLLEWAEKTSKK 65
+F +D + Q LL IE+ EKL ++P ILK YD DILEE+ +L+W EK
Sbjct: 5 KFLAKDEEEQLELLYAIEEFCVEL-EKLGKLLPKILKSLYDADILEEEAILKWYEKA--- 60
Query: 66 YVSKELSAEIRSRAEPFIKWLREA 89
VS E ++R A+PF+ WL+EA
Sbjct: 61 -VSAEGKKKVRKNAKPFVTWLQEA 83
>gnl|CDD|211396 cd11558, W2_eIF2B_epsilon, C-terminal W2 domain of eukaryotic
translation initiation factor 2B epsilon. eIF2B is a
heteropentameric complex which functions as a guanine
nucleotide exchange factor in the recycling of eIF-2
during the initiation of translation in eukaryotes. The
epsilon and gamma subunits are sequence similar and both
are essential in yeast. Epsilon appears to be the
catalytically active subunit, with gamma enhancing its
activity. The C-terminal domain of the eIF2B epsilon
subunit contains bipartite motifs rich in acidic and
aromatic residues, which are responsible for the
interaction with eIF2. The structure of the domain
resembles that of a set of concatenated HEAT repeats.
Length = 169
Score = 60.0 bits (146), Expect = 2e-12
Identities = 29/84 (34%), Positives = 41/84 (48%), Gaps = 3/84 (3%)
Query: 11 DIKAQRYLLNGIEQVIALHKEKLLSMVPGILKLFYDYDILEEKVLLEWAEKTSKKYVSKE 70
Q LL +E+ L E+ + +L YD DILEE+ +LEW E + E
Sbjct: 89 SQDDQVELLLALEEF-CLESEEGGPLFAKLLHALYDLDILEEEAILEWWE--EPDAGADE 145
Query: 71 LSAEIRSRAEPFIKWLREAEEEDS 94
++R + FI+WL EAEEE
Sbjct: 146 EMKKVRELVKKFIEWLEEAEEESD 169
>gnl|CDD|211398 cd11560, W2_eIF5C_like, C-terminal W2 domain of the eukaryotic
translation initiation factor 5C and similar proteins.
eIF5C appears to be essential for the initiation of
protein translation; its actual function, and
specifically that of the C-terminal W2 domain, are not
well understood. The Drosophila ortholog, kra
(krasavietz) or exba (extra bases), may be involved in
translational inhibition in neural development. The
structure of this C-terminal domain resembles that of a
set of concatenated HEAT repeats.
Length = 194
Score = 45.3 bits (108), Expect = 8e-07
Identities = 28/80 (35%), Positives = 42/80 (52%), Gaps = 5/80 (6%)
Query: 13 KAQRYLLNGIEQVIALHKEKLLSMVPGILKLFYDYDILEEKVLLEWAEKTSKKYVSKELS 72
+A+ LLN I Q K + + I+KL Y D+L E +L+W +K K
Sbjct: 120 RAELALLNKI-QEYCYENMKFMKVFQKIVKLLYKADVLSEDAILKWYKKGHS---PKGKQ 175
Query: 73 AEIRSRAEPFIKWLREAEEE 92
++ EPF++WL+EAEEE
Sbjct: 176 VFLKQ-MEPFVEWLQEAEEE 194
>gnl|CDD|211395 cd11473, W2, C-terminal domain of eIF4-gamma/eIF5/eIF2b-epsilon.
This domain is found at the C-terminus of several
translation initiation factors, including the epsilon
chain of eIF2b, where it has been found to catalyze the
conversion of eIF2.GDP to its active eIF2.GTP form. The
structure of the domain resembles that of a set of
concatenated HEAT repeats.
Length = 135
Score = 33.2 bits (76), Expect = 0.012
Identities = 20/47 (42%), Positives = 30/47 (63%), Gaps = 1/47 (2%)
Query: 13 KAQRYLLNGIEQV-IALHKEKLLSMVPGILKLFYDYDILEEKVLLEW 58
K Q YLL IE++ + L +L+S++ IL L YD D+L E+ +L W
Sbjct: 88 KDQLYLLLKIEKLCLQLKLSELISLLEKILDLLYDADVLSEEAILSW 134
>gnl|CDD|143317 cd07693, Ig1_Robo, First immunoglobulin (Ig)-like domain in Robo
(roundabout) receptors and similar proteins. Ig1_Robo:
domain similar to the first immunoglobulin (Ig)-like
domain in Robo (roundabout) receptors. Robo receptors
play a role in the development of the central nervous
system (CNS), and are receptors of Slit protein. Slit is
a repellant secreted by the neural cells in the midline.
Slit acts through Robo to prevent most neurons from
crossing the midline from either side. Three mammalian
Robo homologs (robo1, -2, and -3), and three mammalian
Slit homologs (Slit-1,-2, -3), have been identified.
Commissural axons, which cross the midline, express low
levels of Robo; longitudinal axons, which avoid the
midline, express high levels of Robo. robo1, -2, and -3
are expressed by commissural neurons in the vertebrate
spinal cord and Slits 1, -2, -3 are expressed at the
ventral midline. Robo-3 is a divergent member of the
Robo family which instead of being a positive regulator
of slit responsiveness, antagonizes slit responsiveness
in precrossing axons. The Slit-Robo interaction is
mediated by the second leucine-rich repeat (LRR) domain
of Slit and the two N-terminal Ig domains of Robo, Ig1
and Ig2. The primary Robo binding site for Slit2 has
been shown by surface plasmon resonance experiments and
mutational analysis to be is the Ig1 domain, while the
Ig2 domain has been proposed to harbor a weak secondary
binding site.
Length = 100
Score = 31.4 bits (71), Expect = 0.035
Identities = 15/49 (30%), Positives = 27/49 (55%), Gaps = 4/49 (8%)
Query: 71 LSAEIRSRAEPFIKWLREAEEEDSDSEESDDD---LPNLGALTFGKVVH 116
L+ + R P I+WL+ + ++D ++ LP+ G+L F +VVH
Sbjct: 21 LNCKAEGRPTPTIQWLKNGQPLETDKDDPRSHRIVLPS-GSLFFLRVVH 68
>gnl|CDD|218379 pfam05009, EBV-NA3, Epstein-Barr virus nuclear antigen 3 (EBNA-3).
This family contains EBNA-3A, -3B, and -3C which are
latent infection nuclear proteins important for
Epstein-Barr virus (EBV)-induced B-cell immortalisation
and the immune response to EBV infection.
Length = 254
Score = 29.3 bits (66), Expect = 0.48
Identities = 9/15 (60%), Positives = 12/15 (80%)
Query: 90 EEEDSDSEESDDDLP 104
E EDS+SE D++LP
Sbjct: 221 ESEDSESESDDEELP 235
>gnl|CDD|211397 cd11559, W2_eIF4G1_like, C-terminal W2 domain of eukaryotic
translation initiation factor 4 gamma 1 and similar
proteins. eIF4G1 is a component of the multi-subunit
eukaryotic translation initiation factor 4F, which
facilitates recruitment of the mRNA to the ribosome, a
rate-limiting step during translation initiation. This
C-terminal domain, whose structure resembles that of a
set of concatenated HEAT repeats, has been associated
with binding to/recruiting the kinase Mnk1, which
phosphorylates eIF4E.
Length = 134
Score = 27.6 bits (62), Expect = 1.1
Identities = 15/58 (25%), Positives = 25/58 (43%), Gaps = 7/58 (12%)
Query: 6 RFTHEDIKAQRYLLNGIEQVIALHKEK---LLSMVPGILKLFYDYDILEEKVLLEWAE 60
++ +D + Q L + Q + E LL YD D++EE+ L+W E
Sbjct: 76 KYLDDDEQLQLQALYAL-QALVHTLEFPKGLLLR---FFDALYDEDVIEEEAFLKWKE 129
>gnl|CDD|223009 PHA03211, PHA03211, serine/threonine kinase US3; Provisional.
Length = 461
Score = 27.5 bits (61), Expect = 1.9
Identities = 14/35 (40%), Positives = 20/35 (57%), Gaps = 3/35 (8%)
Query: 69 KELSAEIRSRAEPFIKWLREAEEEDSDSEESDDDL 103
+EL AE+RS E AE ED D +++ DD+
Sbjct: 72 QELLAEMRSSEEYPDS---GAEAEDDDDDDAPDDV 103
>gnl|CDD|152492 pfam12057, DUF3538, Domain of unknown function (DUF3538). This
presumed domain is functionally uncharacterized. This
domain is found in eukaryotes. This domain is about 120
amino acids in length. This domain is found associated
with pfam00240. This domain has a conserved SDL sequence
motif.
Length = 118
Score = 26.3 bits (58), Expect = 3.4
Identities = 9/51 (17%), Positives = 22/51 (43%), Gaps = 7/51 (13%)
Query: 74 EIRSRAEPFIKWLRE-------AEEEDSDSEESDDDLPNLGALTFGKVVHA 117
++ R +PF++ + +E D+ E+D + + + + HA
Sbjct: 10 RVQERLQPFLQRYYDILQNDPTFDENDTQGRENDQRIFDRVSEALHYLSHA 60
>gnl|CDD|115108 pfam06431, Polyoma_lg_T_C, Polyomavirus large T antigen C-terminus.
Length = 417
Score = 26.9 bits (59), Expect = 3.5
Identities = 13/50 (26%), Positives = 23/50 (46%), Gaps = 4/50 (8%)
Query: 55 LLEWAEKTSKK---YVSKELSAEIRSRAEPFIKWLREAEEEDSDSEESDD 101
++EW E+ K+ Y ++ + + + WLRE + ED DS
Sbjct: 332 IVEWKERLDKEISMYTFSKMKFNV-AMGIGILDWLREEDSEDEDSGHGSS 380
>gnl|CDD|143266 cd05858, Ig3_FGFR-2, Third immunoglobulin (Ig)-like domain of
fibroblast growth factor receptor 2 (FGFR2).
Ig3_FGFR-2-like; domain similar to the third
immunoglobulin (Ig)-like domain of human fibroblast
growth factor receptor 2 (FGFR2). Fibroblast growth
factors (FGFs) participate in morphogenesis,
development, angiogenesis, and wound healing. These
FGF-stimulated processes are mediated by four FGFR
tyrosine kinases (FGRF1-4). FGFRs are comprised of an
extracellular portion consisting of three Ig-like
domains, a transmembrane helix, and a cytoplasmic
portion having protein tyrosine kinase activity. The
highly conserved Ig-like domains 2 and 3, and the linker
region between D2 and D3 define a general binding site
for FGFs. FGFR2 is required for male sex determination.
Length = 90
Score = 25.7 bits (56), Expect = 3.5
Identities = 13/40 (32%), Positives = 22/40 (55%), Gaps = 2/40 (5%)
Query: 70 ELSAEIRSRAEPFIKWLREAEEEDSDSEESDDDLPNLGAL 109
E ++ S A+P I+WL+ E+ + S+ D LP + L
Sbjct: 5 EFVCKVYSDAQPHIQWLKHVEK--NGSKYGPDGLPYVTVL 42
>gnl|CDD|220266 pfam09492, Pec_lyase, Pectic acid lyase. Members of this family
are isozymes of pectate lyase (EC:4.2.2.2), also called
polygalacturonic transeliminase and
alpha-1,4-D-endopolygalacturonic acid lyase.
Length = 285
Score = 26.8 bits (60), Expect = 3.5
Identities = 10/33 (30%), Positives = 14/33 (42%)
Query: 70 ELSAEIRSRAEPFIKWLREAEEEDSDSEESDDD 102
+ S EI + E + WL + E DDD
Sbjct: 194 QPSPEILAAIEAAVAWLESVKLPGIRVERIDDD 226
>gnl|CDD|224664 COG1750, COG1750, Archaeal serine proteases [General function
prediction only].
Length = 579
Score = 26.7 bits (59), Expect = 4.0
Identities = 14/59 (23%), Positives = 25/59 (42%)
Query: 49 ILEEKVLLEWAEKTSKKYVSKELSAEIRSRAEPFIKWLREAEEEDSDSEESDDDLPNLG 107
I E + L+ A+ + + +A + RA WL AE++ S S+ L +
Sbjct: 333 IAEAEAELDNAKANGDYDEAVQDAAYAKERAASAELWLSLAEKDASGKIISEAVLKKVA 391
>gnl|CDD|239776 cd04243, AAK_AK-HSDH-like, AAK_AK-HSDH-like: Amino Acid Kinase
Superfamily (AAK), AK-HSDH-like; this family includes
the N-terminal catalytic domain of aspartokinase (AK) of
the bifunctional enzyme AK- homoserine dehydrogenase
(HSDH). These aspartokinases are found in such bacteria
as E. coli (AKI-HSDHI, ThrA and AKII-HSDHII, MetL) and
in higher plants (Z. mays AK-HSDH). AK and HSDH are the
first and third enzymes in the biosynthetic pathway of
the aspartate family of amino acids. AK catalyzes the
phosphorylation of Asp to P-aspartyl phosphate. HSDH
catalyzes the NADPH-dependent conversion of Asp
3-semialdehyde to homoserine. ThrA and MetL are involved
in threonine and methionine biosynthesis, respectively.
In E. coli, ThrA is subject to allosteric regulation by
the end product L-threonine and the native enzyme is
reported to be tetrameric. As with bacteria, plant AK
and HSDH are feedback inhibited by pathway end products.
Maize AK-HSDH is a Thr-sensitive 180-kD enzyme.
Arabidopsis AK-HSDH is an alanine-activated,
threonine-sensitive enzyme whose ACT domains, located
C-terminal to the AK catalytic domain, were shown to be
involved in allosteric activation. Also included in this
CD is the catalytic domain of the aspartokinase (AK) of
the lysine-sensitive aspartokinase isoenzyme AKIII, a
monofunctional class enzyme (LysC) found in some
bacteria such as E. coli. In E. coli, LysC is reported
to be a homodimer of 50 kD subunits. Also included in
this CD is the catalytic domain of aspartokinase (AK)
of the bifunctional enzyme AK - DAP decarboxylase
(DapDC) found in some bacteria. DapDC, which is the lysA
gene product, catalyzes the decarboxylation of DAP to
lysine.
Length = 293
Score = 26.4 bits (59), Expect = 4.1
Identities = 17/59 (28%), Positives = 19/59 (32%), Gaps = 1/59 (1%)
Query: 55 LLEWAEKT-SKKYVSKELSAEIRSRAEPFIKWLREAEEEDSDSEESDDDLPNLGALTFG 112
L+ AE S + EIR R IK L E D L L L G
Sbjct: 46 LVALAELAASGDDAQAIVLQEIRERHLDLIKELLSGESAAELLAALDSLLERLKDLLEG 104
>gnl|CDD|119256 pfam10736, DUF2527, Protein of unknown function (DUF2627). This
family of proteins with unknown function appears to be
restricted to a family of Enterobacterial proteins. It
has a highly conserved sequence.
Length = 38
Score = 24.7 bits (53), Expect = 4.3
Identities = 9/21 (42%), Positives = 15/21 (71%)
Query: 63 SKKYVSKELSAEIRSRAEPFI 83
SK+ +SK++ E R A+P+I
Sbjct: 6 SKEVLSKDVDVEYRFSADPYI 26
>gnl|CDD|131421 TIGR02368, dimeth_PyL, dimethylamine:corrinoid methyltransferase.
This family consists of dimethylamine methyltransferases
from the genus Methanosarcina. It is found in three
nearly identical copies in each of M. acetivorans, M.
barkeri, and M. Mazei. It is one of a suite of three
non-homologous enzymes with a critical UAG-encoded
pyrrolysine residue in these species (along with
trimethylamine methyltransferase and monomethylamine
methyltransferase). It demethylates dimethylamine,
leaving monomethylamine, and methylates the prosthetic
group of the small corrinoid protein MtbC. The methyl
group is then transferred by methylcorrinoid:coenzyme M
methyltransferase to coenzyme M. Note that the
pyrrolysine residue is variously translated as K or X,
or as a stop codon that truncates the sequence.
Length = 466
Score = 26.5 bits (58), Expect = 4.7
Identities = 11/32 (34%), Positives = 20/32 (62%), Gaps = 2/32 (6%)
Query: 61 KTSKKYVSKELSAEIRSRAEPFIKWLREAEEE 92
+K+YV+K+L+ +I A+ + +RE EE
Sbjct: 397 GEAKEYVAKKLNVDIMDLADEHV--MRELREE 426
>gnl|CDD|211710 TIGR02035, D_Ser_am_lyase, D-serine ammonia-lyase. This family
consists of D-serine ammonia-lyase (EC 4.3.1.18), a
pyridoxal-phosphate enzyme that converts D-serine to
pyruvate and NH3. This enzyme is also called D-serine
dehydratase and D-serine deaminase and was previously
designated EC 4.2.1.14. It is homologous to an enzyme
that acts on threonine and may itself act weakly on
threonine [Energy metabolism, Amino acids and amines].
Length = 431
Score = 26.3 bits (58), Expect = 5.1
Identities = 19/42 (45%), Positives = 25/42 (59%), Gaps = 6/42 (14%)
Query: 12 IKAQRYLLNGIEQVIALHKEKLLSMVPGILKLFYDYDILEEK 53
IKA+ GI +V+A H EKL ++ G+L L DY IL E
Sbjct: 109 IKAR----GGIYEVLA-HAEKL-ALEAGLLTLDDDYSILAEP 144
>gnl|CDD|220063 pfam08895, DUF1840, Domain of unknown function (DUF1840). This
family of proteins are functionally uncharacterized.
Length = 105
Score = 25.6 bits (57), Expect = 5.3
Identities = 9/21 (42%), Positives = 11/21 (52%)
Query: 75 IRSRAEPFIKWLREAEEEDSD 95
+ RA P I LR A +E D
Sbjct: 82 LAQRAYPLIDMLRAAAKEGCD 102
>gnl|CDD|219900 pfam08553, VID27, VID27 cytoplasmic protein. This is a family of
fungal and plant proteins and contains many hypothetical
proteins. VID27 is a cytoplasmic protein that plays a
potential role in vacuolar protein degradation.
Length = 794
Score = 26.3 bits (58), Expect = 5.4
Identities = 11/47 (23%), Positives = 20/47 (42%), Gaps = 2/47 (4%)
Query: 58 WAE--KTSKKYVSKELSAEIRSRAEPFIKWLREAEEEDSDSEESDDD 102
W + +T + Y+ SA A E +EE+ + E+ D+
Sbjct: 361 WTKAKETEQDYILDAFSALEIEDANTERDDEEEEDEEEEEEEDEDEG 407
>gnl|CDD|239375 cd03077, GST_N_Alpha, GST_N family, Class Alpha subfamily; GSTs are
cytosolic dimeric proteins involved in cellular
detoxification by catalyzing the conjugation of
glutathione (GSH) with a wide range of endogenous and
xenobiotic alkylating agents, including carcinogens,
therapeutic drugs, environmental toxins and products of
oxidative stress. The GST fold contains an N-terminal
TRX-fold domain and a C-terminal alpha helical domain,
with an active site located in a cleft between the two
domains. The class Alpha subfamily is composed of
eukaryotic GSTs which can form homodimer and
heterodimers. There are at least six types of class
Alpha GST subunits in rats, four of which have human
counterparts, resulting in many possible isoenzymes with
different activities, tissue distribution and substrate
specificities. Human GSTA1-1 and GSTA2-2 show high GSH
peroxidase activity. GSTA3-3 catalyzes the isomerization
of intermediates in steroid hormone biosynthesis.
GSTA4-4 preferentially catalyzes the GSH conjugation of
alkenals.
Length = 79
Score = 25.2 bits (55), Expect = 5.7
Identities = 17/49 (34%), Positives = 24/49 (48%), Gaps = 6/49 (12%)
Query: 76 RSRAEPFIKWLREA-----EEEDSDSEESDDDLPNLGALTFGKVVHAEL 119
R R E I+WL A EE+ +S E + L G+L F +V E+
Sbjct: 10 RGRMES-IRWLLAAAGVEFEEKFIESAEDLEKLKKDGSLMFQQVPMVEI 57
>gnl|CDD|226941 COG4575, ElaB, Uncharacterized conserved protein [Function
unknown].
Length = 104
Score = 25.4 bits (56), Expect = 6.0
Identities = 11/45 (24%), Positives = 19/45 (42%), Gaps = 6/45 (13%)
Query: 52 EKVLLEWAEKTSKKYVSKELSAEIRSRAEPFIKWLREAEEEDSDS 96
E+VL + E+RS+AE +K R+ + D+
Sbjct: 25 EEVLKSSGSLAGDEA------EELRSKAESALKEARDRLGDTGDA 63
>gnl|CDD|215104 PLN00207, PLN00207, polyribonucleotide nucleotidyltransferase;
Provisional.
Length = 891
Score = 26.0 bits (57), Expect = 6.4
Identities = 18/47 (38%), Positives = 25/47 (53%), Gaps = 9/47 (19%)
Query: 50 LEEKVLLEWAEKTSKKYVSKELS-AEIRSRAEPFIKWLREAEEEDSD 95
LEEKV + T + YVSK+ S +RA+ L E E+ED +
Sbjct: 348 LEEKV---LSILTEEGYVSKDESFGTSETRAD-----LLEDEDEDEE 386
>gnl|CDD|238237 cd00405, PRAI, Phosphoribosylanthranilate isomerase (PRAI)
catalyzes the fourth step of the tryptophan
biosynthesis, the conversion of N-(5'-
phosphoribosyl)-anthranilate (PRA) to
1-(o-carboxyphenylamino)- 1-deoxyribulose 5-phosphate
(CdRP). Most PRAIs are monomeric, monofunctional and
thermolabile, but in some thermophile organisms PRAI is
dimeric for reasons of stability and in others it is
fused to other components of the tryptophan
biosynthesis pathway to form multifunctional enzymes.
Length = 203
Score = 25.6 bits (57), Expect = 7.8
Identities = 10/22 (45%), Positives = 14/22 (63%)
Query: 63 SKKYVSKELSAEIRSRAEPFIK 84
S +YVS E + EI + PF+K
Sbjct: 31 SPRYVSPEQAREIVAALPPFVK 52
>gnl|CDD|143322 cd07698, IgC_MHC_I_alpha3, Class I major histocompatibility complex
(MHC) alpha chain immunoglobulin domain.
IgC_MHC_I_alpha3; Immunoglobulin (Ig) domain of major
histocompatibility complex (MHC) class I alpha chain.
Class I MHC proteins bind antigenic peptide fragments
and present them to CD8+ T lymphocytes. Class I
molecules consist of a transmembrane alpha chain and a
small chain called the beta2 microglobulin. The alpha
chain contains three extracellular domains, two of which
fold together to form the peptide-binding cleft (alpha1
and alpha2), and one which has an Ig fold (alpha3).
Peptide binding to class I molecules occurs in the
endoplasmic reticulum (ER) and involves both chaperones
and dedicated factors to assist in peptide loading.
Class I MHC molecules are expressed on most nucleated
cells.
Length = 93
Score = 24.9 bits (55), Expect = 7.8
Identities = 10/23 (43%), Positives = 13/23 (56%), Gaps = 1/23 (4%)
Query: 83 IKWLREAEEEDSDSEESDDDLPN 105
+ WLR E+ D ES + LPN
Sbjct: 33 VTWLR-DGEDSVDDVESGEILPN 54
>gnl|CDD|234923 PRK01222, PRK01222, N-(5'-phosphoribosyl)anthranilate isomerase;
Provisional.
Length = 210
Score = 25.5 bits (57), Expect = 8.1
Identities = 10/22 (45%), Positives = 15/22 (68%)
Query: 63 SKKYVSKELSAEIRSRAEPFIK 84
S +YVS E +AE+ + PF+K
Sbjct: 35 SPRYVSPEQAAELAAALPPFVK 56
>gnl|CDD|222927 PHA02774, PHA02774, E1; Provisional.
Length = 613
Score = 25.6 bits (57), Expect = 8.1
Identities = 11/23 (47%), Positives = 15/23 (65%)
Query: 85 WLREAEEEDSDSEESDDDLPNLG 107
+L EAE E SD E+ +DL + G
Sbjct: 17 FLVEAEAECSDGEDELEDLFDTG 39
>gnl|CDD|225590 COG3048, DsdA, D-serine dehydratase [Amino acid transport and
metabolism].
Length = 443
Score = 25.5 bits (56), Expect = 9.5
Identities = 17/42 (40%), Positives = 24/42 (57%), Gaps = 6/42 (14%)
Query: 12 IKAQRYLLNGIEQVIALHKEKLLSMVPGILKLFYDYDILEEK 53
IKA+ GI +V+ H EKL ++ G+L L DY IL +
Sbjct: 117 IKAR----GGIYEVLK-HAEKL-ALEAGLLTLEDDYSILLSE 152
>gnl|CDD|233830 TIGR02350, prok_dnaK, chaperone protein DnaK. Members of this
family are the chaperone DnaK, of the DnaK-DnaJ-GrpE
chaperone system. All members of the seed alignment were
taken from completely sequenced bacterial or archaeal
genomes and (except for Mycoplasma sequence) found
clustered with other genes of this systems. This model
excludes DnaK homologs that are not DnaK itself, such as
the heat shock cognate protein HscA (TIGR01991).
However, it is not designed to distinguish among DnaK
paralogs in eukaryotes. Note that a number of dnaK genes
have shadow ORFs in the same reverse (relative to dnaK)
reading frame, a few of which have been assigned
glutamate dehydrogenase activity. The significance of
this observation is unclear; lengths of such shadow ORFs
are highly variable as if the presumptive protein
product is not conserved [Protein fate, Protein folding
and stabilization].
Length = 595
Score = 25.3 bits (56), Expect = 9.6
Identities = 13/36 (36%), Positives = 20/36 (55%), Gaps = 1/36 (2%)
Query: 59 AEKTSKKYVSKELSAEIRSRAEPFIKWLREAEEEDS 94
AEKT K+ K L AE + + E + L+EA + +
Sbjct: 537 AEKTLKEAGDK-LPAEEKEKIEKAVAELKEALKGED 571
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 0.387
Gapped
Lambda K H
0.267 0.0740 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,574,583
Number of extensions: 593085
Number of successful extensions: 1062
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1040
Number of HSP's successfully gapped: 98
Length of query: 125
Length of database: 10,937,602
Length adjustment: 85
Effective length of query: 40
Effective length of database: 7,167,512
Effective search space: 286700480
Effective search space used: 286700480
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: 53 (24.2 bits)