RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8137
(88 letters)
>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 = 70.4 bits (173), Expect = 3e-17
Identities = 22/41 (53%), Positives = 32/41 (78%)
Query: 16 LFCHSLHFPKGMLLRWFNNLYNLEIIEEEAFSKWRENISDA 56
H+L FPKG+LLR+F+ LY+ ++IEEEAF KW+E++ A
Sbjct: 94 ALVHTLEFPKGLLLRFFDALYDEDVIEEEAFLKWKEDVDPA 134
>gnl|CDD|214705 smart00515, eIF5C, Domain at the C-termini of GCD6, eIF-2B
epsilon, eIF-4 gamma and eIF-5.
Length = 83
Score = 58.8 bits (143), Expect = 3e-13
Identities = 22/63 (34%), Positives = 31/63 (49%), Gaps = 1/63 (1%)
Query: 15 ELFCHSLHFPKGMLLRWFNNLYNLEIIEEEAFSKWRENISDAYPGKGEALFQVNAWLNWL 74
E FC L +L + +LY+ +I+EEEA KW E A GK + ++ WL
Sbjct: 22 EEFCVELEKLGKLLPKILKSLYDADILEEEAILKWYEKAVSA-EGKKKVRKNAKPFVTWL 80
Query: 75 AEA 77
EA
Sbjct: 81 QEA 83
>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 = 57.6 bits (140), Expect = 7e-13
Identities = 22/66 (33%), Positives = 31/66 (46%), Gaps = 4/66 (6%)
Query: 15 ELFCHSLHFP-KGMLLRWFNNLYNLEIIEEEAFSKWRENISDAYPGKGEALF--QVNAWL 71
E FC + +L + LY+L+I+EEEA KW E G+G Q ++
Sbjct: 11 ERFCGKENPELIKLLPKILKLLYDLDILEEEAILKWYEKSKKV-DGEGSKKVRKQAKPFV 69
Query: 72 NWLAEA 77
WL EA
Sbjct: 70 TWLEEA 75
>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 = 41.9 bits (99), Expect = 5e-06
Identities = 17/49 (34%), Positives = 25/49 (51%), Gaps = 1/49 (2%)
Query: 35 LYNLEIIEEEAFSKWRENISDAY-PGKGEALFQVNAWLNWLAEAESEEE 82
LY+L+I+EEEA +W E + V ++ WL EAE E +
Sbjct: 121 LYDLDILEEEAILEWWEEPDAGADEEMKKVRELVKKFIEWLEEAEEESD 169
>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 = 38.4 bits (90), Expect = 7e-05
Identities = 20/51 (39%), Positives = 27/51 (52%), Gaps = 3/51 (5%)
Query: 35 LYNLEIIEEEAFSKWRENISDAYPGKG---EALFQVNAWLNWLAEAESEEE 82
LY+ +I+EEE KW E +S Y K + ++ WL EAE EEE
Sbjct: 107 LYDNDILEEEVILKWYEKVSKKYVSKEKSKKVRKAAEPFVEWLEEAEEEEE 157
>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 = 31.0 bits (71), Expect = 0.044
Identities = 19/61 (31%), Positives = 30/61 (49%), Gaps = 10/61 (16%)
Query: 22 HFPKGMLLRWFNNLYNLEIIEEEAFSKWRENISDAYPGKGEALF--QVNAWLNWLAEAES 79
F K + L LY +++ E+A KW + KG+ +F Q+ ++ WL EAE
Sbjct: 142 VFQKIVKL-----LYKADVLSEDAILKW---YKKGHSPKGKQVFLKQMEPFVEWLQEAEE 193
Query: 80 E 80
E
Sbjct: 194 E 194
>gnl|CDD|188444 TIGR03929, T7_esaA_Nterm, type VII secretion protein EsaA,
N-terminal domain. Members of this family are
associated with type VII secretion of WXG100 family
targets in the Firmicutes, but not in the
Actinobacteria. This model represents the conserved
N-terminal domain.
Length = 193
Score = 28.1 bits (63), Expect = 0.38
Identities = 13/52 (25%), Positives = 25/52 (48%)
Query: 33 NNLYNLEIIEEEAFSKWRENISDAYPGKGEALFQVNAWLNWLAEAESEEEEE 84
N Y+ ++ FSK ++ P K +++NA N + + E+E+E
Sbjct: 84 NGTYDAMVVIPSDFSKKALSVDKENPEKATLQYKINANGNAVLKEEAEKEAS 135
>gnl|CDD|237246 PRK12881, acnA, aconitate hydratase; Provisional.
Length = 889
Score = 28.0 bits (63), Expect = 0.53
Identities = 11/32 (34%), Positives = 16/32 (50%)
Query: 51 ENISDAYPGKGEALFQVNAWLNWLAEAESEEE 82
EN+ GK + A NWL E +S++E
Sbjct: 47 ENLLRNEDGKKVTEEHLEALANWLPERKSDDE 78
>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 = 27.4 bits (61), Expect = 0.74
Identities = 6/15 (40%), Positives = 10/15 (66%)
Query: 35 LYNLEIIEEEAFSKW 49
LY+ +++ EEA W
Sbjct: 120 LYDADVLSEEAILSW 134
>gnl|CDD|212659 cd07770, FGGY_GntK, Gluconate kinases; a subfamily of the FGGY
family of carbohydrate kinases. This subfamily is
composed of a group of gluconate kinases (GntK, also
known as gluconokinase; EC 2.7.1.12) encoded by the gntK
gene, which catalyzes the ATP-dependent phosphorylation
of D-gluconate and produce 6-phospho-D-gluconate and
ADP. The presence of Mg2+ might be required for
catalytic activity. The prototypical member of this
subfamily is GntK from Lactobacillus acidophilus. Unlike
Escherichia coli GntK, which belongs to the superfamily
of P-loop containing nucleoside triphosphate hydrolases,
members in this subfamily are homologous to glycerol
kinase, xylulose kinase, and rhamnulokinase from
Escherichia coli. They have been classified as members
of the FGGY family of carbohydrate kinases, which
contain two large domains separated by a deep cleft that
forms the active site. This model spans both the
N-terminal domain, which adopts a ribonuclease H-like
fold, and the structurally related C-terminal domain.
Some uncharacterized homologous sequences are also
included in this subfamily. The Lactobacillus gnt operon
contains a single gntK gene. The gnt operons of some
bacteria, such as Corynebacterium glutamicum, have two
gntK genes. For example, the C. glutamicum gnt operon
has both a gluconate kinase gntV gene (also known as
gntK) and a second hypothetical gntK gene (also known as
gntK2). Both gluconate kinases encoded by these genes
belong to this family, however the protein encoded by C.
glutamicum gntV is not included in this model as it is
truncated in the C-terminal domain.
Length = 440
Score = 27.2 bits (61), Expect = 1.1
Identities = 20/73 (27%), Positives = 27/73 (36%), Gaps = 17/73 (23%)
Query: 6 NTPPTATPPELFCHSL---HF-------PKGMLLRWF-NNLYNLEIIEEEAFSKWRENIS 54
+ P T P LFC+ L + G++LRW + L E E E E
Sbjct: 267 DQPVTDPPGRLFCYRLDKGRWVLGGAVNNGGIVLRWLRDTLALPEEEEAE------ELGI 320
Query: 55 DAYPGKGEALFQV 67
D Y G L +
Sbjct: 321 DPYDGLTRGLEFL 333
>gnl|CDD|176220 cd08259, Zn_ADH5, Alcohol dehydrogenases of the MDR family.
NAD(P)(H)-dependent oxidoreductases are the major
enzymes in the interconversion of alcohols and
aldehydes, or ketones. This group contains proteins
that share the characteristic catalytic and structural
zinc-binding sites of the zinc-dependent alcohol
dehydrogenase family. Alcohol dehydrogenase in the
liver converts ethanol and NAD+ to acetaldehyde and
NADH, while in yeast and some other microorganisms ADH
catalyzes the conversion acetaldehyde to ethanol in
alcoholic fermentation. ADH is a member of the medium
chain alcohol dehydrogenase family (MDR), which have a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. The NAD(H)-binding region is
comprised of 2 structurally similar halves, each of
which contacts a mononucleotide. A GxGxxG motif after
the first mononucleotide contact half allows the close
contact of the coenzyme with the ADH backbone. The
N-terminal catalytic domain has a distant homology to
GroES. These proteins typically form dimers (typically
higher plants, mammals) or tetramers (yeast, bacteria),
and have 2 tightly bound zinc atoms per subunit, a
catalytic zinc at the active site and a structural zinc
in a lobe of the catalytic domain. NAD(H)-binding
occurs in the cleft between the catalytic and
coenzyme-binding domains at the active site, and
coenzyme binding induces a conformational closing of
this cleft. Coenzyme binding typically precedes and
contributes to substrate binding. In human ADH
catalysis, the zinc ion helps coordinate the alcohol,
followed by deprotonation of a histidine (His-51), the
ribose of NAD, a serine (Ser-48), then the alcohol,
which allows the transfer of a hydride to NAD+,
creating NADH and a zinc-bound aldehyde or ketone. In
yeast and some bacteria, the active site zinc binds an
aldehyde, polarizing it, and leading to the reverse
reaction.
Length = 332
Score = 26.9 bits (60), Expect = 1.3
Identities = 9/19 (47%), Positives = 11/19 (57%)
Query: 51 ENISDAYPGKGEALFQVNA 69
E + D PG GE L +V A
Sbjct: 16 EEVPDPEPGPGEVLIKVKA 34
>gnl|CDD|240285 PTZ00135, PTZ00135, 60S acidic ribosomal protein P0; Provisional.
Length = 310
Score = 25.7 bits (57), Expect = 3.3
Identities = 9/13 (69%), Positives = 9/13 (69%)
Query: 75 AEAESEEEEEEEE 87
A A EEEEEEE
Sbjct: 289 AAAAPAEEEEEEE 301
Score = 25.0 bits (55), Expect = 5.4
Identities = 9/13 (69%), Positives = 11/13 (84%)
Query: 75 AEAESEEEEEEEE 87
A A +EEEEEEE+
Sbjct: 290 AAAPAEEEEEEED 302
>gnl|CDD|232953 TIGR00392, ileS, isoleucyl-tRNA synthetase. The isoleucyl tRNA
synthetase (IleS) is a class I amino acyl-tRNA ligase
and is particularly closely related to the valyl tRNA
synthetase. This model may recognize IleS from every
species, including eukaryotic cytosolic and
mitochondrial forms [Protein synthesis, tRNA
aminoacylation].
Length = 861
Score = 25.8 bits (57), Expect = 3.3
Identities = 9/26 (34%), Positives = 13/26 (50%), Gaps = 2/26 (7%)
Query: 32 FNNLYNLEIIEEEAFSKWRENISDAY 57
F NL EE+ + W+EN D +
Sbjct: 2 FPMRGNLSKREEKILAFWQEN--DIF 25
>gnl|CDD|235302 PRK04456, PRK04456, acetyl-CoA decarbonylase/synthase complex
subunit beta; Reviewed.
Length = 463
Score = 25.8 bits (57), Expect = 3.6
Identities = 12/16 (75%), Positives = 12/16 (75%)
Query: 72 NWLAEAESEEEEEEEE 87
W AE E EEEEEEEE
Sbjct: 401 RWAAEEEEEEEEEEEE 416
>gnl|CDD|235508 PRK05568, PRK05568, flavodoxin; Provisional.
Length = 142
Score = 25.2 bits (55), Expect = 4.0
Identities = 11/32 (34%), Positives = 15/32 (46%)
Query: 39 EIIEEEAFSKWRENISDAYPGKGEALFQVNAW 70
E++EE + E+IS GK LF W
Sbjct: 62 EVLEEGEMEPFVESISSLVKGKKLVLFGSYGW 93
>gnl|CDD|240576 cd12932, RRP7_like, RRP7 domain ribosomal RNA-processing protein
7 (Rrp7p), ribosomal RNA-processing protein 7 homolog A
(Rrp7A), and similar proteins. This CD corresponds to
the RRP7 domain of Rrp7p and Rrp7A. Rrp7p is encoded by
YCL031C gene from Saccharomyces cerevisiae. It is an
essential yeast protein involved in pre-rRNA processing
and ribosome assembly, and is speculated to be required
for correct assembly of rpS27 into the pre-ribosomal
particle. Rrp7A, also termed gastric cancer antigen
Zg14, is the Rrp7p homolog mainly found in Metazoans.
The cellular function of Rrp7A remains unclear
currently. Both Rrp7p and Rrp7A harbor an N-terminal
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), and
a C-terminal RRP7 domain.
Length = 118
Score = 25.3 bits (56), Expect = 4.1
Identities = 11/42 (26%), Positives = 19/42 (45%)
Query: 47 SKWRENISDAYPGKGEALFQVNAWLNWLAEAESEEEEEEEEN 88
KW + P E +V+ ++ + E EE+EE +E
Sbjct: 3 KKWVAEYKRSRPDPAELQSEVDEYMEEFDKREEEEKEEAKEA 44
>gnl|CDD|148846 pfam07471, Phage_Nu1, Phage DNA packaging protein Nu1.
Terminase, the DNA packaging enzyme of bacteriophage
lambda, is a heteromultimer composed of subunits Nu1
and A. The smaller Nu1 terminase subunit has a
low-affinity ATPase stimulated by non-specific DNA.
Length = 164
Score = 25.2 bits (55), Expect = 4.4
Identities = 12/47 (25%), Positives = 18/47 (38%), Gaps = 3/47 (6%)
Query: 45 AFSKWRENISDAYPGKG---EALFQVNAWLNWLAEAESEEEEEEEEN 88
W+ G G E +F A + W AE ++E E E+
Sbjct: 18 TIDNWQSQGLPVVKGGGKGREVVFDTAAVIRWYAERDAEIENEKLRK 64
>gnl|CDD|240287 PTZ00142, PTZ00142, 6-phosphogluconate dehydrogenase; Provisional.
Length = 470
Score = 25.1 bits (55), Expect = 5.3
Identities = 10/30 (33%), Positives = 17/30 (56%), Gaps = 2/30 (6%)
Query: 28 LLRWFNNLYNLEIIEEEAFSKWRENISDAY 57
L++ + N E+ E F+KW E I ++Y
Sbjct: 202 LMKHILGMSNEEL--SEVFNKWNEGILNSY 229
>gnl|CDD|187851 cd09720, Cas1_II, CRISPR/Cas system-associated protein Cas1.
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;
Cas1 is the most universal CRISPR system protein thought
to be involved in spacer intergration. Cas1 is
metal-dependent deoxyribonuclease, also binds RNA; Shown
to possess a unique fold consisting of a N-terminal
beta-strand domain and a C-terminal alpha-helical
domain.
Length = 275
Score = 25.3 bits (56), Expect = 5.4
Identities = 10/40 (25%), Positives = 20/40 (50%), Gaps = 2/40 (5%)
Query: 16 LFCHSLHFPKGMLLRWFNNLYNLEIIEEEAFSKWRENISD 55
+FC H P G LL ++ + +L+ ++ + KW +
Sbjct: 63 IFCDEKHLPVGQLLPFYGHHRSLKRLKLQI--KWSDPFKK 100
>gnl|CDD|239654 cd03682, ClC_sycA_like, ClC sycA-like chloride channel proteins.
This ClC family presents in bacteria, where it
facilitates acid resistance in acidic soil. Mutation of
this gene (sycA) in Rhizobium tropici CIAT899 causes
serious deficiencies in nodule development, nodulation
competitiveness, and N2 fixation on Phaseolus vulgaris
plants, due to its reduced ability for acid resistance.
This family is part of the ClC chloride channel
superfamiy. These proteins catalyse the selective flow
of Cl- ions across cell membranes and Cl-/H+ exchange
transport. These proteins share two characteristics that
are apparently inherent to the entire ClC chloride
channel superfamily: a unique double-barreled
architecture and voltage-dependent gating mechanism. The
gating is conferred by the permeating anion itself,
acting as the gating charge.
Length = 378
Score = 25.2 bits (56), Expect = 5.5
Identities = 9/21 (42%), Positives = 11/21 (52%)
Query: 16 LFCHSLHFPKGMLLRWFNNLY 36
LF LHF K +L + N Y
Sbjct: 216 LFAELLHFLKKLLKKRIKNPY 236
>gnl|CDD|224530 COG1614, CdhC, CO dehydrogenase/acetyl-CoA synthase beta subunit
[Energy production and conversion].
Length = 470
Score = 25.2 bits (55), Expect = 6.4
Identities = 11/15 (73%), Positives = 11/15 (73%)
Query: 73 WLAEAESEEEEEEEE 87
W E E EEEEEEEE
Sbjct: 401 WAEEEEEEEEEEEEE 415
>gnl|CDD|224606 COG1692, COG1692, Calcineurin-like phosphoesterase [General
function prediction only].
Length = 266
Score = 24.9 bits (55), Expect = 7.1
Identities = 8/17 (47%), Positives = 11/17 (64%)
Query: 52 NISDAYPGKGEALFQVN 68
N D PGKG +F++N
Sbjct: 90 NYPDGTPGKGSRIFKIN 106
>gnl|CDD|233191 TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger. [Transport and
binding proteins, Cations and iron carrying compounds].
Length = 1096
Score = 25.0 bits (54), Expect = 7.1
Identities = 11/13 (84%), Positives = 11/13 (84%)
Query: 76 EAESEEEEEEEEN 88
E E EEEEEEEEN
Sbjct: 878 EEEEEEEEEEEEN 890
>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 = 24.7 bits (54), Expect = 7.3
Identities = 15/39 (38%), Positives = 21/39 (53%), Gaps = 4/39 (10%)
Query: 50 RENISDAYPGKGEALFQVNAWLNWLAEAESEEEEEEEEN 88
++ I DA+ AL +A E E +EEEEEEE+
Sbjct: 369 QDYILDAF----SALEIEDANTERDDEEEEDEEEEEEED 403
>gnl|CDD|224561 COG1647, COG1647, Esterase/lipase [General function prediction
only].
Length = 243
Score = 24.6 bits (54), Expect = 8.0
Identities = 9/39 (23%), Positives = 15/39 (38%)
Query: 28 LLRWFNNLYNLEIIEEEAFSKWRENISDAYPGKGEALFQ 66
LL +F N E ++E K ++ D L +
Sbjct: 130 LLEYFRNAKKYEGKDQEQIDKEMKSYKDTPMTTTAQLKK 168
>gnl|CDD|237088 PRK12393, PRK12393, amidohydrolase; Provisional.
Length = 457
Score = 24.6 bits (54), Expect = 8.7
Identities = 11/26 (42%), Positives = 13/26 (50%)
Query: 5 PNTPPTATPPELFCHSLHFPKGMLLR 30
P TP + PPEL +GM LR
Sbjct: 208 PTTPTFSLPPELLREVARAARGMGLR 233
>gnl|CDD|182772 PRK10841, PRK10841, hybrid sensory kinase in two-component
regulatory system with RcsB and YojN; Provisional.
Length = 924
Score = 24.5 bits (54), Expect = 9.0
Identities = 10/57 (17%), Positives = 14/57 (24%), Gaps = 12/57 (21%)
Query: 3 PGPNTPPTATP--PELFCHSLHFPKGMLLRWFNNLYNLEIIEEEAFSKWRENISDAY 57
P P + C ++ L WR+N S AY
Sbjct: 71 ETKTDVPAFEPLFADSDCSAMSNTWRGSLESLAWF----------MRYWRDNFSAAY 117
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
0.312 0.132 0.424
Gapped
Lambda K H
0.267 0.0812 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,967,575
Number of extensions: 408350
Number of successful extensions: 737
Number of sequences better than 10.0: 1
Number of HSP's gapped: 713
Number of HSP's successfully gapped: 74
Length of query: 88
Length of database: 10,937,602
Length adjustment: 56
Effective length of query: 32
Effective length of database: 8,453,778
Effective search space: 270520896
Effective search space used: 270520896
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 53 (24.0 bits)