RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14757
(90 letters)
>gnl|CDD|211318 cd11566, eIF1_SUI1, Eukaryotic initiation factor 1. eIF1/SUI1
(eukaryotic initiation factor 1) plays an important
role in accurate initiator codon recognition during
translation initiation. eIF1 interacts with 18S rRNA in
the 40S ribosomal subunit during eukaryotic translation
initiation. Point mutations in the yeast eIF1 implicate
the protein in maintaining accurate start-site
selection but its mechanism of action is unknown.
Length = 84
Score = 102 bits (256), Expect = 2e-30
Identities = 38/47 (80%), Positives = 43/47 (91%)
Query: 16 GLVHIRIQQRNGRKTLTTVQGLSSEYDLKKIVRACKKEFACNGTVIE 62
G +HIRIQQRNGRKTLTTVQGL E+DLKKI++A KKEFACNGTV+E
Sbjct: 1 GYIHIRIQQRNGRKTLTTVQGLPEEFDLKKILKAFKKEFACNGTVVE 47
>gnl|CDD|130228 TIGR01160, SUI1_MOF2, translation initiation factor SUI1,
eukaryotic. Alternate name: MOF2. A similar protein
family (see TIGRFAMs model TIGR01158) is found in
prokaryotes. The human proteins complements a yeast
SUI1 mutatation [Protein synthesis, Translation
factors].
Length = 110
Score = 99.5 bits (248), Expect = 6e-29
Identities = 48/65 (73%), Positives = 51/65 (78%), Gaps = 5/65 (7%)
Query: 1 PFADAFKGSEDDVQDG---LVHIRIQQRNGRKTLTTVQGLSSEYDLKKIVRACKKEFACN 57
PFADA G +D G +HIRIQQRNGRKTLTTVQGL EYDLKKIV+A KKEFACN
Sbjct: 10 PFADA--GDDDSALPGTSNYIHIRIQQRNGRKTLTTVQGLPKEYDLKKIVKALKKEFACN 67
Query: 58 GTVIE 62
GTVIE
Sbjct: 68 GTVIE 72
>gnl|CDD|216391 pfam01253, SUI1, Translation initiation factor SUI1.
Length = 74
Score = 66.8 bits (164), Expect = 2e-16
Identities = 22/48 (45%), Positives = 30/48 (62%), Gaps = 1/48 (2%)
Query: 14 QDGLVHIRIQQRNGRKTLTTVQGL-SSEYDLKKIVRACKKEFACNGTV 60
+D + IR ++R G KT+T V GL DLKK+ + KK+F C GTV
Sbjct: 3 EDQKIRIRREKRRGGKTVTVVTGLELFGIDLKKLAKELKKKFGCGGTV 50
>gnl|CDD|223102 COG0023, SUI1, Translation initiation factor 1 (eIF-1/SUI1) and
related proteins [Translation, ribosomal structure and
biogenesis].
Length = 104
Score = 63.5 bits (155), Expect = 7e-15
Identities = 21/48 (43%), Positives = 30/48 (62%), Gaps = 1/48 (2%)
Query: 14 QDGLVHIRIQQRNGRKTLTTVQGL-SSEYDLKKIVRACKKEFACNGTV 60
D +V IR + R KT+T ++GL + DLKK+ + KK+ AC GTV
Sbjct: 25 GDQIVRIRRETRRKGKTVTIIEGLDLKDIDLKKLAKELKKKCACGGTV 72
>gnl|CDD|211317 cd00474, eIF1_SUI1_like, Eukaryotic initiation factor 1 and
related proteins. Members of the eIF1/SUI1 (eukaryotic
initiation factor 1) family are found in eukaryotes,
archaea, and some bacteria; eukaryotic members are
understood to play an important role in accurate
initiator codon recognition during translation
initiation. eIF1 interacts with 18S rRNA in the 40S
ribosomal subunit during eukaryotic translation
initiation. Point mutations in the yeast eIF1 implicate
the protein in maintaining accurate start-site
selection but its mechanism of action is unknown. The
function of non-eukaryotic family members is also
unclear.
Length = 78
Score = 54.7 bits (132), Expect = 1e-11
Identities = 18/45 (40%), Positives = 30/45 (66%)
Query: 18 VHIRIQQRNGRKTLTTVQGLSSEYDLKKIVRACKKEFACNGTVIE 62
+HI+++QR+G K +T V+GL + DL+K+ KK+ C G+V
Sbjct: 2 IHIKVEQRSGGKKVTKVEGLPAYIDLRKLADELKKKLGCGGSVEG 46
>gnl|CDD|211320 cd11607, DENR_C, C-terminal domain of DENR and related proteins.
DENR (density regulated protein), together with MCT-1
(multiple copies T cell malignancies), has been shown
to have similar function as eIF2D translation
initiation factor (also known as ligatin), which is
involved in the recruitment and delivery of
aminoacyl-tRNAs to the P-site of the eukaryotic
ribosome in a GTP-independent manner.
Length = 86
Score = 42.2 bits (100), Expect = 9e-07
Identities = 20/46 (43%), Positives = 27/46 (58%), Gaps = 1/46 (2%)
Query: 18 VHIRIQQRNGRKTLTTVQGLSSEY-DLKKIVRACKKEFACNGTVIE 62
V I+ RN RK +TTV GL + DLKK + K+FAC +V +
Sbjct: 3 VTIKRISRNKRKFVTTVTGLETFGIDLKKAAKLFAKKFACGASVTK 48
>gnl|CDD|130226 TIGR01158, SUI1_rel, translation initation factor SUI1, putative,
prokaryotic. This family of archaeal and bacterial
proteins is homologous to the eukaryotic translation
intiation factor SUI1 involved in directing the
ribosome to the proper start site of translation by
functioning in concert with eIF-2 and the initiator
tRNA-Met [Protein synthesis, Translation factors].
Length = 101
Score = 39.6 bits (93), Expect = 2e-05
Identities = 19/54 (35%), Positives = 31/54 (57%), Gaps = 4/54 (7%)
Query: 10 EDDVQDGLVHIRIQQRNGR--KTLTTVQGLS-SEYDLKKIVRACKKEFACNGTV 60
+D +V I+ + R GR K +T ++GL S+ DLK++ + K + C GTV
Sbjct: 18 AKPKEDQVVRIQRETR-GRKGKGVTIIEGLDLSDIDLKELAKELKSKCGCGGTV 70
>gnl|CDD|211321 cd11608, eIF2D_C, C-terminal domain of eIF2D and related
proteins. eIF2D translation initiation factor (also
known as ligatin) is involved in the recruitment and
delivery of aminoacyl-tRNAs to the P-site of the
eukaryotic ribosome in a GTP-independent manner.
Length = 85
Score = 37.2 bits (87), Expect = 9e-05
Identities = 12/48 (25%), Positives = 25/48 (52%), Gaps = 1/48 (2%)
Query: 18 VHIRIQQRNGRKTLTTVQGLSS-EYDLKKIVRACKKEFACNGTVIEVS 64
+ I ++R G K +T + GL S D ++ + +K+ A + +V +
Sbjct: 2 IDITTERRQGNKKVTLISGLESFGIDPEEFAKELQKKCAASTSVSPLP 49
>gnl|CDD|179173 PRK00939, PRK00939, translation initiation factor Sui1; Reviewed.
Length = 99
Score = 36.8 bits (86), Expect = 1e-04
Identities = 14/44 (31%), Positives = 27/44 (61%), Gaps = 1/44 (2%)
Query: 18 VHIRIQQRNGRKTLTTVQGLS-SEYDLKKIVRACKKEFACNGTV 60
+ I++ +R K +T ++G+ + DLK++ + K + AC GTV
Sbjct: 26 IKIKVDKRRYGKEVTIIEGIDPKDIDLKELAKKLKSKLACGGTV 69
>gnl|CDD|211319 cd11567, YciH_like, Homologs of eIF1/SUI1 including Escherichia
coli YciH. Members of the eIF1/SUI1 (eukaryotic
initiation factor 1) family are found in eukaryotes,
archaea, and some bacteria; eukaryotic members are
understood to play an important role in accurate
initiator codon recognition during translation
initiation. The function of non-eukaryotic family
members is unclear. Escherichia coli YciH is a
non-essential protein and was reported to be able to
perform some of the functions of IF3 in prokaryotic
initiation.
Length = 76
Score = 34.4 bits (80), Expect = 7e-04
Identities = 20/49 (40%), Positives = 32/49 (65%), Gaps = 2/49 (4%)
Query: 16 GLVHIRIQQR-NGRKTLTTVQGLS-SEYDLKKIVRACKKEFACNGTVIE 62
V +R+++R G KT+T ++GL SE DLK++ + KK+ C GTV +
Sbjct: 1 QKVRVRLEKRGRGGKTVTVIEGLPLSEEDLKELAKELKKKCGCGGTVKD 49
>gnl|CDD|181613 PRK09019, PRK09019, translation initiation factor Sui1;
Validated.
Length = 108
Score = 29.2 bits (66), Expect = 0.12
Identities = 23/60 (38%), Positives = 32/60 (53%), Gaps = 10/60 (16%)
Query: 15 DGLVHIRIQ-QRNGRK--TLTTVQGLS-SEYDLKKIVRACKKEFACNGTV----IEVSRD 66
DG+V RIQ Q +GRK + + GL + +LKK+ KK+ C G V IE+ D
Sbjct: 30 DGIV--RIQRQTSGRKGKGVCLITGLDLDDAELKKLAAELKKKCGCGGAVKDGVIEIQGD 87
>gnl|CDD|233294 TIGR01159, DRP1, density-regulated protein DRP1. This protein
family shows weak but suggestive similarity to
translation initiation factor SUI1 and its prokaryotic
homologs.
Length = 173
Score = 28.7 bits (64), Expect = 0.30
Identities = 15/45 (33%), Positives = 26/45 (57%), Gaps = 1/45 (2%)
Query: 18 VHIRIQQRNGRKTLTTVQGLSS-EYDLKKIVRACKKEFACNGTVI 61
V I+ + R RK +T ++GL + + DLKK + ++FA +V
Sbjct: 91 VTIKREPRTKRKFVTVIKGLETFDIDLKKASKTFAQKFATGCSVS 135
>gnl|CDD|214444 MTH00165, ND5, NADH dehydrogenase subunit 5; Provisional.
Length = 573
Score = 28.6 bits (65), Expect = 0.41
Identities = 8/14 (57%), Positives = 11/14 (78%), Gaps = 2/14 (14%)
Query: 36 GLSS--EYDLKKIV 47
GL + E+DLKKI+
Sbjct: 258 GLGANFEFDLKKII 271
>gnl|CDD|213992 cd07437, PHP_HisPPase_Ycdx_like, Polymerase and Histidinol
Phosphatase domain of Ycdx like. PHP Ycdx-like is a
stand alone PHP domain similar to Ycdx E. coli protein
with an unknown physiological role. The PHP (also called
histidinol phosphatase-2/HIS2) domain is associated with
several types of DNA polymerases, such as PolIIIA and
family X DNA polymerases, stand alone histidinol
phosphate phosphatases (HisPPases), and a number of
uncharacterized protein families. The PHP domain has
four conserved sequence motifs and contains an invariant
histidine that is involved in metal ion coordination. It
has also been shown that the PHP domain functions in DNA
repair. The PHP structures have a distorted
(beta/alpha)7 barrel fold with a trinuclear metal site
on the C-terminal side of the barrel. YcdX may be
involved in swarming.
Length = 233
Score = 26.3 bits (59), Expect = 1.9
Identities = 5/24 (20%), Positives = 12/24 (50%), Gaps = 4/24 (16%)
Query: 40 EYDLKKIVRACKKEFACNGTVIEV 63
D + +V+A K+ ++E+
Sbjct: 137 PIDYEAVVKAAKE----YNVLLEI 156
>gnl|CDD|181036 PRK07568, PRK07568, aspartate aminotransferase; Provisional.
Length = 397
Score = 26.0 bits (58), Expect = 2.8
Identities = 13/34 (38%), Positives = 17/34 (50%), Gaps = 5/34 (14%)
Query: 52 KEFACNGTVIEVSRDTFPLCDFYRATPSRGKNRV 85
+F NG + V+ P FY ATP GKN +
Sbjct: 340 TDFNYNGETVMVA----PASGFY-ATPGLGKNEI 368
>gnl|CDD|235270 PRK04286, PRK04286, hypothetical protein; Provisional.
Length = 298
Score = 26.1 bits (58), Expect = 2.9
Identities = 15/43 (34%), Positives = 19/43 (44%), Gaps = 5/43 (11%)
Query: 23 QQRNGRKTLTTVQGLSSEYDLKKIVRACKKEFACNGTVIEVSR 65
Q+R + L V+ + KKI A K F GT IE S
Sbjct: 117 QRRRAPRFLKAVKDI-----AKKIEYADGKTFRFGGTTIEFSP 154
>gnl|CDD|236881 PRK11202, PRK11202, DNA-binding transcriptional repressor FabR;
Provisional.
Length = 203
Score = 25.0 bits (55), Expect = 5.5
Identities = 9/26 (34%), Positives = 16/26 (61%)
Query: 43 LKKIVRACKKEFACNGTVIEVSRDTF 68
L++++R ++ A G+VI S TF
Sbjct: 71 LRQLMRQARQRIAKGGSVIRTSVSTF 96
>gnl|CDD|240433 PTZ00482, PTZ00482, membrane-attack complex/perforin (MACPF)
Superfamily; Provisional.
Length = 844
Score = 25.2 bits (55), Expect = 6.0
Identities = 10/27 (37%), Positives = 16/27 (59%)
Query: 27 GRKTLTTVQGLSSEYDLKKIVRACKKE 53
GR+ T+ QG S++YD+ I C +
Sbjct: 642 GREKCTSKQGSSNKYDVSYIYIECGPQ 668
>gnl|CDD|215603 PLN03145, PLN03145, Protein phosphatase 2c; Provisional.
Length = 365
Score = 25.3 bits (55), Expect = 6.3
Identities = 9/22 (40%), Positives = 12/22 (54%)
Query: 50 CKKEFACNGTVIEVSRDTFPLC 71
C+ G IE+SRD P+C
Sbjct: 188 CRAVLCRRGKAIEMSRDHKPMC 209
>gnl|CDD|239447 cd03331, Macro_Poa1p_like_SNF2, Macro domain, Poa1p_like family,
SNF2 subfamily. The macro domain is a high-affinity
ADP-ribose binding module found in a variety of proteins
as a stand-alone domain or in combination with other
domains like in histone macroH2A and some PARPs (poly
ADP-ribose polymerases). Some macro domains recognize
poly ADP-ribose as a ligand. Previously identified as
displaying an Appr-1"-p (ADP-ribose-1"-monophosphate)
processing activity, the macro domain may play roles in
distinct ADP-ribose pathways, such as the
ADP-ribosylation of proteins, an important
post-translational modification which occurs in DNA
repair, transcription, chromatin biology, and long-term
memory formation, among other processes. Members of this
subfamily contain a C-terminal macro domain that show
similarity to the yeast protein Poa1p, reported to be a
phosphatase specific for Appr-1"-p, a tRNA splicing
metabolite. In addition, they also contain an SNF2
domain, defined by the presence of seven motifs with
sequence similarity to DNA helicases. SNF2 proteins have
the capacity to use the energy released by their
DNA-dependent ATPase activity to stabilize or perturb
protein-DNA interactions and play important roles in
transcriptional regulation, maintenance of chromosome
integrity and DNA repair.
Length = 152
Score = 24.8 bits (54), Expect = 6.9
Identities = 15/54 (27%), Positives = 24/54 (44%), Gaps = 3/54 (5%)
Query: 7 KGSEDDVQDGLVHIRIQQRNGRKTLTTVQGLSSEYDLKKIVRACKKEFACNGTV 60
K S D + I Q R+ L+ ++ + E LKKI A K+ + +V
Sbjct: 74 KNSRLKGPDWVALIVAQHRDKSNPLSGIKLSALEKGLKKIYFAAKQ---KSASV 124
>gnl|CDD|163685 cd07948, DRE_TIM_HCS, Saccharomyces cerevisiae homocitrate synthase
and related proteins, catalytic TIM barrel domain.
Homocitrate synthase (HCS) catalyzes the condensation of
acetyl-CoA and alpha-ketoglutarate to form homocitrate,
the first step in the lysine biosynthesis pathway. This
family includes the Yarrowia lipolytica LYS1 protein as
well as the Saccharomyces cerevisiae LYS20 and LYS21
proteins. This family belongs to the DRE-TIM
metallolyase superfamily. DRE-TIM metallolyases include
2-isopropylmalate synthase (IPMS), alpha-isopropylmalate
synthase (LeuA), 3-hydroxy-3-methylglutaryl-CoA lyase,
homocitrate synthase, citramalate synthase,
4-hydroxy-2-oxovalerate aldolase, re-citrate synthase,
transcarboxylase 5S, pyruvate carboxylase, AksA, and
FrbC. These members all share a conserved
triose-phosphate isomerase (TIM) barrel domain
consisting of a core beta(8)-alpha(8) motif with the
eight parallel beta strands forming an enclosed barrel
surrounded by eight alpha helices. The domain has a
catalytic center containing a divalent cation-binding
site formed by a cluster of invariant residues that cap
the core of the barrel. In addition, the catalytic site
includes three invariant residues - an aspartate (D), an
arginine (R), and a glutamate (E) - which is the basis
for the domain name "DRE-TIM".
Length = 262
Score = 25.0 bits (55), Expect = 7.0
Identities = 28/94 (29%), Positives = 39/94 (41%), Gaps = 25/94 (26%)
Query: 17 LVHIRIQQRNGRKTLTT-VQGLS-----SEY--------DLKKIVRACKK--EFACNGTV 60
L HIR + R + T V G+ S + + +I+ + + EF +
Sbjct: 67 LTHIRCHMDDARIAVETGVDGVDLVFGTSPFLREASHGKSITEIIESAVEVIEFVKSKG- 125
Query: 61 IEV---SRDTF--PLCD---FYRATPSRGKNRVG 86
IEV S D+F L D YRA G NRVG
Sbjct: 126 IEVRFSSEDSFRSDLVDLLRVYRAVDKLGVNRVG 159
>gnl|CDD|132967 cd06636, STKc_MAP4K4_6, Catalytic domain of the Protein
Serine/Threonine Kinases, Mitogen-Activated Protein
Kinase Kinase Kinase Kinase 4 and 6. Serine/threonine
kinases (STKs), mitogen-activated protein kinase (MAPK)
kinase kinase kinase 4 (MAPKKKK4 or MAP4K4) and MAPKKKK6
(or MAP4K6) subfamily, catalytic (c) domain. STKs
catalyze the transfer of the gamma-phosphoryl group from
ATP to serine/threonine residues on protein substrates.
The MAP4K4/MAP4K6 subfamily is part of a larger
superfamily that includes the catalytic domains of other
protein STKs, protein tyrosine kinases, RIO kinases,
aminoglycoside phosphotransferase, choline kinase, and
phosphoinositide 3-kinase. Members of this subfamily
contain an N-terminal catalytic domain and a C-terminal
citron homology (CNH) regulatory domain. MAP4Ks (or
MAPKKKKs) are involved in MAPK signaling pathways that
are important in mediating cellular responses to
extracellular signals by activating a MAPK kinase kinase
(MAPKKK or MAP3K or MKKK). Each MAPK cascade is
activated either by a small GTP-binding protein or by an
adaptor protein, which transmits the signal either
directly to a MAP3K to start the triple kinase core
cascade or indirectly through a mediator kinase, a
MAP4K. MAP4K4 is also called Nck Interacting kinase
(NIK). It facilitates the activation of the MAPKs,
extracellular signal-regulated kinase (ERK) 1, ERK2, and
c-Jun N-terminal kinase (JNK), by phosphorylating and
activating MEKK1. MAP4K4 plays a role in tumor necrosis
factor (TNF) alpha-induced insulin resistance. MAP4K4
silencing in skeletal muscle cells from type II diabetic
patients restores insulin-mediated glucose uptake.
MAP4K4, through JNK, also plays a broad role in cell
motility, which impacts inflammation, homeostasis, as
well as the invasion and spread of cancer. MAP4K4 is
found to be highly expressed in most tumor cell lines
relative to normal tissue. MAP4K6 (also called MINK for
Misshapen/NIKs-related kinase) is activated after Ras
induction and mediates activation of p38 MAPK. MAP4K6
plays a role in cell cycle arrest, cytoskeleton
organization, cell adhesion, and cell motility.
Length = 282
Score = 25.0 bits (54), Expect = 7.4
Identities = 12/37 (32%), Positives = 18/37 (48%), Gaps = 3/37 (8%)
Query: 54 FACNGTVIEVSRDTFPLCDFYRATPSRGKNRVGGNPP 90
++ T IE++ PLCD + P R + NPP
Sbjct: 210 WSLGITAIEMAEGAPPLCDMH---PMRALFLIPRNPP 243
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
0.319 0.137 0.413
Gapped
Lambda K H
0.267 0.0717 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,425,551
Number of extensions: 339479
Number of successful extensions: 298
Number of sequences better than 10.0: 1
Number of HSP's gapped: 295
Number of HSP's successfully gapped: 23
Length of query: 90
Length of database: 10,937,602
Length adjustment: 58
Effective length of query: 32
Effective length of database: 8,365,070
Effective search space: 267682240
Effective search space used: 267682240
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 (21.7 bits)
S2: 53 (24.2 bits)