RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8661
(71 letters)
>gnl|CDD|177670 PLN00036, PLN00036, 40S ribosomal protein S4; Provisional.
Length = 261
Score = 131 bits (332), Expect = 3e-40
Identities = 53/69 (76%), Positives = 59/69 (85%)
Query: 1 MLDKLGGVFAPRPSTGPHKLRESLPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRT 60
MLDKLGG FAP+PS+GPHK RE LPL++ LRNRLKYALT +EV ILMQR +KVDGKVRT
Sbjct: 19 MLDKLGGAFAPKPSSGPHKKRECLPLLLILRNRLKYALTYREVQAILMQRHVKVDGKVRT 78
Query: 61 DTNYPAGFM 69
D YPAGFM
Sbjct: 79 DKTYPAGFM 87
>gnl|CDD|240277 PTZ00118, PTZ00118, 40S ribosomal protein S4; Provisional.
Length = 262
Score = 111 bits (279), Expect = 3e-32
Identities = 50/69 (72%), Positives = 57/69 (82%)
Query: 1 MLDKLGGVFAPRPSTGPHKLRESLPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRT 60
MLDKLGG +AP+ S GPHKLRE LPLVI LRNRLKYALT EV I++Q+++KVDGKVRT
Sbjct: 19 MLDKLGGQYAPKTSPGPHKLRECLPLVILLRNRLKYALTYDEVKLIVIQKIVKVDGKVRT 78
Query: 61 DTNYPAGFM 69
D YP GFM
Sbjct: 79 DCTYPVGFM 87
>gnl|CDD|224388 COG1471, RPS4A, Ribosomal protein S4E [Translation, ribosomal
structure and biogenesis].
Length = 241
Score = 103 bits (260), Expect = 2e-29
Identities = 33/69 (47%), Positives = 44/69 (63%)
Query: 1 MLDKLGGVFAPRPSTGPHKLRESLPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRT 60
+ + G +A RPS GPHK ESLPL++ +R+ LKYA +E KIL + + VDGKVR
Sbjct: 18 PIPRKTGKWAVRPSPGPHKAEESLPLLVIIRDYLKYADNAREARKILSEGKVLVDGKVRK 77
Query: 61 DTNYPAGFM 69
D +P G M
Sbjct: 78 DYKFPVGLM 86
>gnl|CDD|140250 PTZ00223, PTZ00223, 40S ribosomal protein S4; Provisional.
Length = 273
Score = 95.1 bits (236), Expect = 8e-26
Identities = 47/69 (68%), Positives = 51/69 (73%)
Query: 1 MLDKLGGVFAPRPSTGPHKLRESLPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRT 60
ML KL GVFAPRP GPHKLRE LPL+I +RNRLKYAL +E IL Q L+ VDGK R
Sbjct: 16 MLSKLTGVFAPRPRAGPHKLRECLPLLIIIRNRLKYALNAREAQMILRQGLVCVDGKPRK 75
Query: 61 DTNYPAGFM 69
D YPAGFM
Sbjct: 76 DGKYPAGFM 84
>gnl|CDD|179820 PRK04313, PRK04313, 30S ribosomal protein S4e; Validated.
Length = 237
Score = 81.4 bits (202), Expect = 5e-21
Identities = 27/63 (42%), Positives = 40/63 (63%)
Query: 7 GVFAPRPSTGPHKLRESLPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRTDTNYPA 66
+ +PS GPH + ES+PL++ LR+ L YA T +E KI+ + + VDG+VR D +P
Sbjct: 21 YKWTVKPSPGPHSIEESIPLLVVLRDVLGYADTAREAKKIINEGKVLVDGRVRKDYKFPV 80
Query: 67 GFM 69
G M
Sbjct: 81 GLM 83
>gnl|CDD|191938 pfam08071, RS4NT, RS4NT (NUC023) domain. This is the N-terminal
domain of Ribosomal S4 / S4e proteins. This domain is
associated with S4 and KOW domains.
Length = 38
Score = 42.6 bits (101), Expect = 1e-07
Identities = 15/22 (68%), Positives = 16/22 (72%)
Query: 1 MLDKLGGVFAPRPSTGPHKLRE 22
LDK GG FA +PS GPHK RE
Sbjct: 17 PLDKKGGKFAVKPSPGPHKKRE 38
>gnl|CDD|201819 pfam01479, S4, S4 domain. The S4 domain is a small domain
consisting of 60-65 amino acid residues that was
detected in the bacterial ribosomal protein S4,
eukaryotic ribosomal S9, two families of pseudouridine
synthases, a novel family of predicted RNA methylases,
a yeast protein containing a pseudouridine synthetase
and a deaminase domain, bacterial tyrosyl-tRNA
synthetases, and a number of uncharacterized, small
proteins that may be involved in translation
regulation. The S4 domain probably mediates binding to
RNA.
Length = 48
Score = 31.7 bits (73), Expect = 0.004
Identities = 12/42 (28%), Positives = 21/42 (50%), Gaps = 1/42 (2%)
Query: 24 LPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRTDTNYP 65
+ L L RL A + E +++ ++V+GKV D +Y
Sbjct: 1 MRLDKVLA-RLGLASSRSEARQLIRHGHVRVNGKVVKDPSYR 41
>gnl|CDD|214638 smart00363, S4, S4 RNA-binding domain.
Length = 60
Score = 31.0 bits (71), Expect = 0.007
Identities = 10/33 (30%), Positives = 18/33 (54%)
Query: 33 RLKYALTNQEVLKILMQRLIKVDGKVRTDTNYP 65
RL A + + +++ Q +KV+GK T +Y
Sbjct: 9 RLGLAPSRSQARRLIEQGRVKVNGKKVTKPSYI 41
>gnl|CDD|238095 cd00165, S4, S4/Hsp/ tRNA synthetase RNA-binding domain; The
domain surface is populated by conserved, charged
residues that define a likely RNA-binding site; Found
in stress proteins, ribosomal proteins and tRNA
synthetases; This may imply a hitherto unrecognized
functional similarity between these three protein
classes.
Length = 70
Score = 29.5 bits (67), Expect = 0.033
Identities = 12/40 (30%), Positives = 19/40 (47%), Gaps = 1/40 (2%)
Query: 26 LVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRTDTNYP 65
L L RL A + E +++ + V+GKV T +Y
Sbjct: 3 LDKILA-RLGLAPSRSEARQLIKHGHVLVNGKVVTKPSYK 41
>gnl|CDD|218556 pfam05327, RRN3, RNA polymerase I specific transcription initiation
factor RRN3. This family consists of several eukaryotic
proteins which are homologous to the yeast RRN3 protein.
RRN3 is one of the RRN genes specifically required for
the transcription of rDNA by RNA polymerase I (Pol I) in
Saccharomyces cerevisiae.
Length = 554
Score = 27.7 bits (62), Expect = 0.39
Identities = 15/45 (33%), Positives = 28/45 (62%), Gaps = 8/45 (17%)
Query: 17 PHKLRESLPLVIFLRNRLKYALTN------QEVLKILMQRLIKVD 55
PHK + LV ++RN L+ LT ++L+++++RL+K+D
Sbjct: 173 PHKTKSKKVLVGYVRNLLR--LTEYCPELGFDILELIIERLLKLD 215
>gnl|CDD|223450 COG0373, HemA, Glutamyl-tRNA reductase [Coenzyme metabolism].
Length = 414
Score = 24.9 bits (55), Expect = 4.0
Identities = 10/25 (40%), Positives = 14/25 (56%)
Query: 43 VLKILMQRLIKVDGKVRTDTNYPAG 67
VL L Q+ I V +VR++T G
Sbjct: 133 VLNRLFQKAISVGKRVRSETGIGKG 157
>gnl|CDD|133452 cd05213, NAD_bind_Glutamyl_tRNA_reduct, NADP-binding domain of
glutamyl-tRNA reductase. Glutamyl-tRNA reductase
catalyzes the conversion of glutamyl-tRNA to
glutamate-1-semialdehyde, initiating the synthesis of
tetrapyrrole. Whereas tRNAs are generally associated
with peptide bond formation in protein translation, here
the tRNA activates glutamate in the initiation of
tetrapyrrole biosynthesis in archaea, plants and many
bacteria. In the first step, activated glutamate is
reduced to glutamate-1-semi-aldehyde via the NADPH
dependent glutamyl-tRNA reductase. Glutamyl-tRNA
reductase forms a V-shaped dimer. Each monomer has 3
domains: an N-terminal catalytic domain, a classic
nucleotide binding domain, and a C-terminal dimerization
domain. Although the representative structure 1GPJ lacks
a bound NADPH, a theoretical binding pocket has been
described. (PMID 11172694). Amino acid dehydrogenase
(DH)-like NAD(P)-binding domains are members of the
Rossmann fold superfamily and include glutamate,
leucine, and phenylalanine DHs, methylene
tetrahydrofolate DH, methylene-tetrahydromethanopterin
DH, methylene-tetrahydropholate DH/cyclohydrolase,
Shikimate DH-like proteins, malate oxidoreductases, and
glutamyl tRNA reductase. Amino acid DHs catalyze the
deamination of amino acids to keto acids with NAD(P)+ as
a cofactor. The NAD(P)-binding Rossmann fold superfamily
includes a wide variety of protein families including
NAD(P)- binding domains of alcohol DHs,
tyrosine-dependent oxidoreductases,
glyceraldehyde-3-phosphate DH, lactate/malate DHs,
formate/glycerate DHs, siroheme synthases,
6-phosphogluconate DH, amino acid DHs, repressor rex,
NAD-binding potassium channel domain, CoA-binding, and
ornithine cyclodeaminase-like domains. These domains
have an alpha-beta-alpha configuration. NAD binding
involves numerous hydrogen and van der Waals contacts.
Length = 311
Score = 24.9 bits (55), Expect = 4.2
Identities = 10/21 (47%), Positives = 15/21 (71%)
Query: 42 EVLKILMQRLIKVDGKVRTDT 62
++L L Q+ IKV +VRT+T
Sbjct: 132 KLLNRLFQKAIKVGKRVRTET 152
>gnl|CDD|99857 cd06103, ScCS-like, Saccharomyces cerevisiae (Sc) citrate synthase
(CS)-like. CS catalyzes the condensation of acetyl
coenzyme A (AcCoA) with oxaloacetate (OAA) to form
citrate and coenzyme A (CoA), the first step in the
citric acid cycle (TCA or Krebs cycle). Some CS proteins
function as 2-methylcitrate synthase (2MCS). 2MCS
catalyzes the condensation of propionyl-coenzyme A
(PrCoA) and OAA to form 2-methylcitrate and CoA during
propionate metabolism. The overall CS reaction is
thought to proceed through three partial reactions and
involves both closed and open conformational forms of
the enzyme: a) the carbanion or equivalent is generated
from AcCoA by base abstraction of a proton, b) the
nucleophilic attack of this carbanion on OAA to generate
citryl-CoA, and c) the hydrolysis of citryl-CoA to
produce citrate and CoA. There are two types of CSs:
type I CS and type II CSs. Type I CSs are found in
eukarya, gram-positive bacteria, archaea, and in some
gram-negative bacteria and are homodimers with both
subunits participating in the active site. Type II CSs
are unique to gram-negative bacteria and are
homohexamers of identical subunits (approximated as a
trimer of dimers). This group includes three S.
cerevisiae CS proteins, ScCit1,-2,-3. ScCit1 is a
nuclear-encoded mitochondrial CS with highly specificity
for AcCoA; in addition to having activity with AcCoA, it
plays a part in the construction of the TCA cycle
metabolon. Yeast cells deleted for Cit1 are
hyper-susceptible to apoptosis induced by heat and aging
stress. ScCit2 is a peroxisomal CS involved in the
glyoxylate cycle; in addition to having activity with
AcCoA, it may have activity with PrCoA. ScCit3 is a
mitochondrial CS and functions in the metabolism of
PrCoA; it is a dual specificity CS and 2MCS, having
similar catalytic efficiency with both AcCoA and PrCoA.
The pattern of expression of the ScCIT3 gene follows
that of the ScCIT1 gene and its expression is increased
in the presence of a ScCIT1 deletion. Included in this
group is the Tetrahymena 14 nm filament protein which
functions as a CS in mitochondria and as a cytoskeletal
component in cytoplasm and Geobacter sulfurreducens
(GSu) CS. GSuCS is dimeric and eukaryotic-like; it lacks
2MCS activity and is inhibited by ATP. In contrast to
eukaryotic and other prokaryotic CSs, GSuCIT is not
stimulated by K+ ions. This group contains proteins
which functions exclusively as either a CS or a 2MCS, as
well as those with relaxed specificity which have dual
functions as both a CS and a 2MCS.
Length = 426
Score = 24.6 bits (54), Expect = 5.6
Identities = 12/24 (50%), Positives = 16/24 (66%), Gaps = 1/24 (4%)
Query: 38 LTNQEVLKILMQRLIKVDGKVRTD 61
L NQEVLK L++ + K GK +D
Sbjct: 272 LANQEVLKWLLK-MQKELGKDVSD 294
>gnl|CDD|224573 COG1659, COG1659, Uncharacterized protein, linocin/CFP29 homolog
[Function unknown].
Length = 267
Score = 24.5 bits (53), Expect = 5.9
Identities = 11/26 (42%), Positives = 14/26 (53%)
Query: 2 LDKLGGVFAPRPSTGPHKLRESLPLV 27
+L V AP H+LR+S PLV
Sbjct: 52 TGRLIDVKAPTNEVIAHQLRKSKPLV 77
>gnl|CDD|232974 TIGR00435, cysS, cysteinyl-tRNA synthetase. This model finds the
cysteinyl-tRNA synthetase from most but not from all
species. The enzyme from one archaeal species,
Archaeoglobus fulgidus, is found but the equivalent
enzymes from some other Archaea, including Methanococcus
jannaschii, are not found, although biochemical evidence
suggests that tRNA(Cys) in these species are charged
directly with Cys rather than through a misacylation and
correction pathway as for tRNA(Gln) [Protein synthesis,
tRNA aminoacylation].
Length = 464
Score = 24.3 bits (53), Expect = 6.1
Identities = 9/38 (23%), Positives = 15/38 (39%)
Query: 31 RNRLKYALTNQEVLKILMQRLIKVDGKVRTDTNYPAGF 68
R+ L ++ E K ++RL K + T Y
Sbjct: 298 RSPLDFSEELLEAAKNALERLYKALRVLDTSLAYSGNQ 335
>gnl|CDD|183914 PRK13243, PRK13243, glyoxylate reductase; Reviewed.
Length = 333
Score = 24.4 bits (53), Expect = 6.5
Identities = 13/45 (28%), Positives = 21/45 (46%), Gaps = 6/45 (13%)
Query: 8 VFAPRPSTGPHKLRESLP------LVIFLRNRLKYALTNQEVLKI 46
V AP + + RE + L+ F R + L N+EV+K+
Sbjct: 284 VLAPHIGSATFEAREGMAELVAENLIAFKRGEVPPTLVNREVVKV 328
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
0.325 0.143 0.413
Gapped
Lambda K H
0.267 0.0783 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,685,027
Number of extensions: 279154
Number of successful extensions: 286
Number of sequences better than 10.0: 1
Number of HSP's gapped: 286
Number of HSP's successfully gapped: 17
Length of query: 71
Length of database: 10,937,602
Length adjustment: 41
Effective length of query: 30
Effective length of database: 9,119,088
Effective search space: 273572640
Effective search space used: 273572640
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 (24.1 bits)