RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 031602
(156 letters)
>gnl|CDD|107221 cd06464, ACD_sHsps-like, Alpha-crystallin domain (ACD) of
alpha-crystallin-type small(s) heat shock proteins
(Hsps). sHsps are small stress induced proteins with
monomeric masses between 12 -43 kDa, whose common
feature is the Alpha-crystallin domain (ACD). sHsps are
generally active as large oligomers consisting of
multiple subunits, and are believed to be
ATP-independent chaperones that prevent aggregation and
are important in refolding in combination with other
Hsps.
Length = 88
Score = 79.5 bits (197), Expect = 2e-20
Identities = 39/94 (41%), Positives = 51/94 (54%), Gaps = 6/94 (6%)
Query: 48 DILDSPKDYIFFMDVPGRPKSDIQVTVEDERTLVIRSNGKRKREDGEEEGCKCIRLERRV 107
D+ ++ Y+ D+PG K DI+V VED L I G+R+ E EEE +R ER
Sbjct: 1 DVYETDDAYVVEADLPGFKKEDIKVEVED-GVLTIS--GEREEE--EEEEENYLRRERS- 54
Query: 108 PQKLLRKFKLPEDANVSAISAKCENGVLTIVVEK 141
R F+LPED + I A ENGVLTI + K
Sbjct: 55 YGSFSRSFRLPEDVDPDKIKASLENGVLTITLPK 88
>gnl|CDD|107229 cd06472, ACD_ScHsp26_like, Alpha crystallin domain (ACD) found in
Saccharomyces cerevisiae (Sc) small heat shock protein
(Hsp)26 and similar proteins. sHsps are molecular
chaperones that suppress protein aggregation and protect
against cell stress, and are generally active as large
oligomers consisting of multiple subunits. ScHsp26 is
temperature-regulated, it switches from an inactive to a
chaperone-active form upon elevation in temperature. It
associates into large 24-mers storage forms which upon
heat shock disassociate into dimers. These dimers
initiate the interaction with non-native substrate
proteins and re-assemble into large globular assemblies
having one monomer of substrate bound per dimer. This
group also contains Arabidopsis thaliana (Ath) Hsp15.7,
a peroxisomal matrix protein which can complement the
morphological phenotype of S. cerevisiae mutants
deficient in Hsps26. AthHsp15.7 is minimally expressed
under normal conditions and is strongly induced by heat
and oxidative stress. Also belonging to this group is
wheat HSP16.9 which differs in quaternary structure from
the shell-type particles of ScHsp26, it assembles as a
dodecameric double disc, with each disc organized as a
trimer of dimers.
Length = 92
Score = 78.1 bits (193), Expect = 8e-20
Identities = 41/95 (43%), Positives = 63/95 (66%), Gaps = 4/95 (4%)
Query: 47 VDILDSPKDYIFFMDVPGRPKSDIQVTVEDERTLVIRSNGKRKREDGEEEGCKCIRLERR 106
VD ++P+ ++F DVPG K D++V VED R L I +G+RK+E+ E++G R+ER
Sbjct: 2 VDWKETPEAHVFKADVPGVKKEDVKVEVEDGRVLRI--SGERKKEE-EKKGDDWHRVERS 58
Query: 107 VPQKLLRKFKLPEDANVSAISAKCENGVLTIVVEK 141
+ +R+F+LPE+A+ + A ENGVLT+ V K
Sbjct: 59 -SGRFVRRFRLPENADADEVKAFLENGVLTVTVPK 92
>gnl|CDD|223149 COG0071, IbpA, Molecular chaperone (small heat shock protein)
[Posttranslational modification, protein turnover,
chaperones].
Length = 146
Score = 79.3 bits (196), Expect = 1e-19
Identities = 47/143 (32%), Positives = 70/143 (48%), Gaps = 11/143 (7%)
Query: 12 VNHLFDIPETMEKFTTPSRSPHQETNKSKGVSSIPVDILDSPKDYIFFMDVPGRPKSDIQ 71
L D P F +S+ + PVDI ++ +Y ++PG K DI+
Sbjct: 13 FPLLRDSPGFDRLF-----REFGNLPESRPTGTPPVDIEETDDEYRITAELPGVDKEDIE 67
Query: 72 VTVEDERTLVIRSNGKRKREDGEEEGCKCIRLERRVPQKLLRKFKLPEDANVSAISAKCE 131
+TVE TL IR G+R+ E+ EEE + R + R F+LPE + I AK +
Sbjct: 68 ITVE-GNTLTIR--GEREEEEEEEE--EGYLRRERAYGEFERTFRLPEKVDPEVIKAKYK 122
Query: 132 NGVLTIVVEKLPP-PPKPKTVEV 153
NG+LT+ + K P KPK +E+
Sbjct: 123 NGLLTVTLPKAEPEEKKPKRIEI 145
>gnl|CDD|215655 pfam00011, HSP20, Hsp20/alpha crystallin family.
Length = 101
Score = 77.6 bits (192), Expect = 1e-19
Identities = 38/107 (35%), Positives = 61/107 (57%), Gaps = 8/107 (7%)
Query: 48 DILDSPKDYIFFMDVPGRPKSDIQVTVEDERTLVIRSNGKRKREDGEEEGCKCIRLERRV 107
DI + ++ +DVPG +++V VED R LV GK ++E+ ++ G + R R
Sbjct: 1 DIKEDKDAFVVKLDVPGFKPEELKVKVEDNRVLVK---GKHEKEEEDDHGLRSERSYR-- 55
Query: 108 PQKLLRKFKLPEDANVSAISAKCENGVLTIVVEKLPPP-PKPKTVEV 153
RKF LPE+A+ + A ++GVLT+ V KL PP KP+ +++
Sbjct: 56 --SFSRKFVLPENADPDKVKASLKDGVLTVTVPKLEPPEKKPRRIQI 100
>gnl|CDD|107219 cd00298, ACD_sHsps_p23-like, This domain family includes the
alpha-crystallin domain (ACD) of alpha-crystallin-type
small heat shock proteins (sHsps) and a similar domain
found in p23-like proteins. sHsps are small stress
induced proteins with monomeric masses between 12 -43
kDa, whose common feature is this ACD. sHsps are
generally active as large oligomers consisting of
multiple subunits, and are believed to be
ATP-independent chaperones that prevent aggregation and
are important in refolding in combination with other
Hsps. p23 is a cochaperone of the Hsp90 chaperoning
pathway. It binds Hsp90 and participates in the folding
of a number of Hsp90 clients including the progesterone
receptor. p23 also has a passive chaperoning activity.
p23 in addition may act as the cytosolic prostaglandin
E2 synthase. Included in this family is the p23-like
C-terminal CHORD-SGT1 (CS) domain of suppressor of G2
allele of Skp1 (Sgt1) and the p23-like domains of human
butyrate-induced transcript 1 (hB-ind1), NUD (nuclear
distribution) C, Melusin, and NAD(P)H cytochrome b5
(NCB5) oxidoreductase (OR).
Length = 80
Score = 63.8 bits (156), Expect = 2e-14
Identities = 32/93 (34%), Positives = 44/93 (47%), Gaps = 13/93 (13%)
Query: 49 ILDSPKDYIFFMDVPGRPKSDIQVTVEDERTLVIRSNGKRKREDGEEEGCKCIRLERRVP 108
+ + + +D+PG K DI+V VED L I GKR+ E+ E R
Sbjct: 1 WYQTDDEVVVTVDLPGVKKEDIKVEVED-NVLTIS--GKREEEEERE----------RSY 47
Query: 109 QKLLRKFKLPEDANVSAISAKCENGVLTIVVEK 141
+ R F+LPED + A ENGVL I + K
Sbjct: 48 GEFERSFELPEDVDPEKSKASLENGVLEITLPK 80
>gnl|CDD|107228 cd06471, ACD_LpsHSP_like, Group of bacterial proteins containing an
alpha crystallin domain (ACD) similar to Lactobacillus
plantarum (Lp) small heat shock proteins (sHsp) HSP
18.5, HSP 18.55 and HSP 19.3. sHsps are molecular
chaperones that suppress protein aggregation and protect
against cell stress, and are generally active as large
oligomers consisting of multiple subunits. Transcription
of the genes encoding Lp HSP 18.5, 18.55 and 19.3 is
regulated by a variety of stresses including heat, cold
and ethanol. Early growing L. plantarum cells contain
elevated levels of these mRNAs which rapidly fall of as
the cells enter stationary phase. Also belonging to this
group is Bifidobacterium breve (Bb) HSP20 and Oenococcus
oenis (syn. Leuconostoc oenos) (Oo) HSP18.
Transcription of the gene encoding BbHSP20 is strongly
induced following heat or osmotic shock, and that of the
gene encoding OoHSP18 following heat, ethanol or acid
shock. OoHSP18 is peripherally associated with the
cytoplasmic membrane.
Length = 93
Score = 61.0 bits (149), Expect = 3e-13
Identities = 34/96 (35%), Positives = 49/96 (51%), Gaps = 6/96 (6%)
Query: 47 VDILDSPKDYIFFMDVPGRPKSDIQVTVEDERTLVIRSNGKRKR-EDGEEEGCKCIRLER 105
DI ++ +YI D+PG K DI++ +D L I + KR +D +++ IR ER
Sbjct: 3 TDIKETDDEYIVEADLPGFKKEDIKLDYKDG-YLTI--SAKRDESKDEKDKKGNYIRRER 59
Query: 106 RVPQKLLRKFKLPEDANVSAISAKCENGVLTIVVEK 141
R F LP + + I AK ENGVL I + K
Sbjct: 60 YYGS-FSRSFYLP-NVDEEEIKAKYENGVLKITLPK 93
>gnl|CDD|107227 cd06470, ACD_IbpA-B_like, Alpha-crystallin domain (ACD) found in
Escherichia coli inclusion body-associated proteins IbpA
and IbpB, and similar proteins. IbpA and IbpB are 16
kDa small heat shock proteins (sHsps). sHsps are
molecular chaperones that suppress protein aggregation
and protect against cell stress, and are generally
active as large oligomers consisting of multiple
subunits. IbpA and IbpB are produced during high-level
production of various heterologous proteins,
specifically human prorenin, renin and bovine
insulin-like growth factor 2 (bIGF-2), and are strongly
associated with inclusion bodies containing these
heterologous proteins. IbpA and IbpB work as an
integrated system to stabilize thermally aggregated
proteins in a disaggregation competent state. The
chaperone activity of IbpB is also significantly
elevated as the temperature increases from normal to
heat shock. The high temperature results in the
disassociation of 2-3-MDa IbpB oligomers into smaller
approximately 600-kDa structures. This elevated activity
seen under heat shock conditions is retained for an
extended period of time after the temperature is
returned to normal. IbpA also forms multimers.
Length = 90
Score = 37.9 bits (89), Expect = 2e-04
Identities = 24/80 (30%), Positives = 40/80 (50%), Gaps = 12/80 (15%)
Query: 60 MDVPGRPKSDIQVTVEDERTLVIRSNGKRKREDGEEE--GCKCIRLERRVPQKLLRKFKL 117
+ V G + D+++ VE+ L + GK+ E+ EE + I +R + R F L
Sbjct: 17 LAVAGFSEDDLEIEVEN-NQLTVT--GKKADEENEEREYLHRGIA--KRAFE---RSFNL 68
Query: 118 PEDANVSAISAKCENGVLTI 137
+ +V A+ ENG+LTI
Sbjct: 69 AD--HVKVKGAELENGLLTI 86
>gnl|CDD|107247 cd06526, metazoan_ACD, Alpha-crystallin domain (ACD) of metazoan
alpha-crystallin-type small(s) heat shock proteins
(Hsps). sHsps are small stress induced proteins with
monomeric masses between 12 -43 kDa, whose common
feature is the Alpha-crystallin domain (ACD). sHsps are
generally active as large oligomers consisting of
multiple subunits, and are believed to be
ATP-independent chaperones that prevent aggregation and
are important in refolding in combination with other
Hsps.
Length = 83
Score = 36.3 bits (85), Expect = 6e-04
Identities = 23/91 (25%), Positives = 43/91 (47%), Gaps = 13/91 (14%)
Query: 48 DILDSPKDYIFFMDVPGRPKSDIQVTVEDERTLVIRSNGKRKREDGEEEGCKCIRLERRV 107
+ D + + +DV G +++V V D LV+ K E+ E+E R
Sbjct: 1 VVNDDDEKFQVTLDVKGFKPEELKVKVSD-NKLVVEG----KHEEREDEHGYVSR----- 50
Query: 108 PQKLLRKFKLPEDANVSAISAK-CENGVLTI 137
+ R+++LPE + ++++ +GVLTI
Sbjct: 51 --EFTRRYQLPEGVDPDSVTSSLSSDGVLTI 79
>gnl|CDD|187652 cd08948, 5beta-POR_like_SDR_a, progesterone 5-beta-reductase-like
proteins (5beta-POR), atypical (a) SDRs. 5beta-POR
catalyzes the reduction of progesterone to
5beta-pregnane-3,20-dione in Digitalis plants. This
subgroup of atypical-extended SDRs, shares the
structure of an extended SDR, but has a different
glycine-rich nucleotide binding motif (GXXGXXG) and
lacks the YXXXK active site motif of classical and
extended SDRs. Tyr-179 and Lys 147 are present in the
active site, but not in the usual SDR configuration.
Given these differences, it has been proposed that this
subfamily represents a new SDR class. Other atypical
SDRs include biliverdin IX beta reductase (BVR-B,aka
flavin reductase), NMRa (a negative transcriptional
regulator of various fungi), phenylcoumaran benzylic
ether and pinoresinol-lariciresinol reductases,
phenylpropene synthases, eugenol synthase,
triphenylmethane reductase, isoflavone reductases, and
others. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving
as a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton
relay involving the conserved Tyr and Lys, a water
molecule stabilized by Asn, and nicotinamide. In
addition to the Rossmann fold core region typical of
all SDRs, extended SDRs have a less conserved
C-terminal extension of approximately 100 amino acids,
and typically have a TGXXGXXG cofactor binding motif.
Complex (multidomain) SDRs such as ketoreductase
domains of fatty acid synthase have a GGXGXXG
NAD(P)-binding motif and an altered active site motif
(YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 308
Score = 33.0 bits (76), Expect = 0.037
Identities = 15/46 (32%), Positives = 19/46 (41%)
Query: 10 AAVNHLFDIPETMEKFTTPSRSPHQETNKSKGVSSIPVDILDSPKD 55
A V HL P T K SR P + + V I +D+LD
Sbjct: 14 ALVEHLLSDPGTWWKVYGLSRRPLPTEDDPRLVEHIGIDLLDPADT 59
>gnl|CDD|217325 pfam03028, Dynein_heavy, Dynein heavy chain and region D6 of dynein
motor. This family represents the C-terminal region of
dynein heavy chain. The chain also contains ATPase
activity and microtubule binding ability and acts as a
motor for the movement of organelles and vesicles along
microtubules. Dynein is also involved in cilia and
flagella movement. The dynein subunit consists of at
least two heavy chains and a number of intermediate and
light chains. The 380 kDa motor unit of dynein belongs
to the AAA class of chaperone-like ATPases. The core of
the 380 kDa motor unit contains a concatenated chain of
six AAA modules, of which four correspond to the ATP
binding sites with P-loop signatures described
previously, and two are modules in which the P loop has
been lost in evolution. This C-terminal domain carries
the D6 region of the dynein motor where the P-loop has
been lost in evolution but the general structure of a
potential ATP binding site appears to be retained.
Length = 706
Score = 33.1 bits (76), Expect = 0.043
Identities = 9/31 (29%), Positives = 13/31 (41%)
Query: 4 VIDDVAAAVNHLFDIPETMEKFTTPSRSPHQ 34
V+ D+ + LF I E K T + P
Sbjct: 442 VLRDILEKLPKLFPIEEIKLKRTEEIKDPLF 472
>gnl|CDD|216809 pfam01958, DUF108, Domain of unknown function DUF108. This family
has no known function. It is found to compose the
complete protein in archaebacteria and a single domain
in a large C. elegans protein.
Length = 91
Score = 29.5 bits (67), Expect = 0.22
Identities = 12/31 (38%), Positives = 16/31 (51%)
Query: 120 DANVSAISAKCENGVLTIVVEKLPPPPKPKT 150
D N+ I + + G I VE +P P PKT
Sbjct: 51 DRNIHEIEVRGDFGEFVIRVENVPSPDNPKT 81
>gnl|CDD|182691 PRK10743, PRK10743, heat shock protein IbpA; Provisional.
Length = 137
Score = 29.8 bits (67), Expect = 0.30
Identities = 16/42 (38%), Positives = 26/42 (61%), Gaps = 3/42 (7%)
Query: 113 RKFKLPEDANVSAISAKCENGVLTIVVEKL-PPPPKPKTVEV 153
RKF+L E+ +V A NG+L I +E++ P KP+ +E+
Sbjct: 97 RKFQLAENIHVRG--ANLVNGLLYIDLERVIPEAKKPRRIEI 136
>gnl|CDD|173862 cd08497, PBP2_NikA_DppA_OppA_like_14, The substrate-binding
component of an uncharacterized ABC-type
nickel/dipeptide/oligopeptide-like import system
contains the type 2 periplasmic binding fold. This CD
represents the substrate-binding domain of an
uncharacterized ATP-binding cassette (ABC) type
nickel/dipeptide/oligopeptide-like transporter. The
oligopeptide-binding protein OppA and the
dipeptide-binding protein DppA show significant sequence
similarity to NikA, the initial nickel receptor. The
DppA binds dipeptides and some tripeptides and is
involved in chemotaxis toward dipeptides, whereas the
OppA binds peptides of a wide range of lengths (2-35
amino acid residues) and plays a role in recycling of
cell wall peptides, which precludes any involvement in
chemotaxis. Most of other periplasmic binding proteins
are comprised of only two globular subdomains
corresponding to domains I and III of the
dipeptide/oligopeptide binding proteins. The structural
topology of these domains is most similar to that of the
type 2 periplasmic binding proteins (PBP2), which are
responsible for the uptake of a variety of substrates
such as phosphate, sulfate, polysaccharides,
lysine/arginine/ornithine, and histidine. The PBP2 bind
their ligand in the cleft between these domains in a
manner resembling a Venus flytrap. After binding their
specific ligand with high affinity, they can interact
with a cognate membrane transport complex comprised of
two integral membrane domains and two cytoplasmically
located ATPase domains. This interaction triggers the
ligand translocation across the cytoplasmic membrane
energized by ATP hydrolysis. Besides transport
proteins, the PBP2 superfamily includes the
ligand-binding domains from ionotropic glutamate
receptors, LysR-type transcriptional regulators, and
unorthodox sensor proteins involved in signal
transduction.
Length = 491
Score = 28.6 bits (65), Expect = 1.2
Identities = 11/46 (23%), Positives = 18/46 (39%), Gaps = 9/46 (19%)
Query: 55 DYIFFMDV---PGRP-----KSDI-QVTVEDERTLVIRSNGKRKRE 91
D +F + G P +D+ +V D+ T+ K RE
Sbjct: 98 DVVFSFETLKSKGPPYYRAYYADVEKVEALDDHTVRFTFKEKANRE 143
>gnl|CDD|178693 PLN03148, PLN03148, Blue copper-like protein; Provisional.
Length = 167
Score = 28.3 bits (63), Expect = 1.3
Identities = 11/19 (57%), Positives = 14/19 (73%), Gaps = 1/19 (5%)
Query: 130 CENGV-LTIVVEKLPPPPK 147
C NG+ +TI+V LPPPP
Sbjct: 107 CFNGMKVTILVHPLPPPPS 125
>gnl|CDD|115057 pfam06375, BLVR, Bovine leukaemia virus receptor (BLVR). This
family consists of several bovine specific leukaemia
virus receptors which are thought to function as
transmembrane proteins, although their exact function is
unknown.
Length = 561
Score = 28.5 bits (63), Expect = 1.6
Identities = 22/80 (27%), Positives = 33/80 (41%), Gaps = 4/80 (5%)
Query: 29 SRSPHQETNKSKGVSSIPVDILDSPKDYIFFMDVPGRPKSDIQVTVEDERTLVIRSNGKR 88
S SP + GV IPV +D + VPG P SD V +E+ER R +
Sbjct: 43 SPSPQKRYQDPPGVEHIPVVQIDLSVP----LKVPGLPMSDQYVKLEEERRHRQRLEKDK 98
Query: 89 KREDGEEEGCKCIRLERRVP 108
+ + E+ + R +
Sbjct: 99 REKKKREKEKRGRRRHHSLG 118
>gnl|CDD|234743 PRK00390, leuS, leucyl-tRNA synthetase; Validated.
Length = 805
Score = 27.7 bits (63), Expect = 2.7
Identities = 11/24 (45%), Positives = 16/24 (66%)
Query: 66 PKSDIQVTVEDERTLVIRSNGKRK 89
P +D VEDE T+V++ NGK +
Sbjct: 733 PTADEAALVEDEVTIVVQVNGKVR 756
>gnl|CDD|224995 COG2084, MmsB, 3-hydroxyisobutyrate dehydrogenase and related
beta-hydroxyacid dehydrogenases [Lipid metabolism].
Length = 286
Score = 27.6 bits (62), Expect = 2.8
Identities = 9/20 (45%), Positives = 10/20 (50%)
Query: 120 DANVSAISAKCENGVLTIVV 139
DA VS G LTI+V
Sbjct: 118 DAPVSGGVPGAAAGTLTIMV 137
>gnl|CDD|218762 pfam05816, TelA, Toxic anion resistance protein (TelA). This
family consists of several prokaryotic TelA like
proteins. TelA and KlA are associated with tellurite
resistance and plasmid fertility inhibition.
Length = 333
Score = 27.5 bits (62), Expect = 3.2
Identities = 15/46 (32%), Positives = 28/46 (60%), Gaps = 5/46 (10%)
Query: 69 DIQVTVEDERTLVIRSNGKRKREDGEEEGCKCIRLERRVPQKLLRK 114
++ T+++ TL I+ G++KR+ E+E +LE + Q+LLR
Sbjct: 292 NLIETIDE--TLQIQEEGRQKRKQAEKE---LEQLEEELKQRLLRA 332
>gnl|CDD|234187 TIGR03369, cellulose_bcsE, cellulose biosynthesis protein BcsE.
This protein, called BcsE (bacterial cellulose synthase
E) or YhjS, is required for cellulose biosynthesis in
Salmonella enteritidis. Its role is this process across
multiple bacterial species is implied by the partial
phylogenetic profiling algorithm. Members are found in
the vicinity of other cellulose biosynthesis genes. The
model does not include a much less well-conserved
N-terminal region about 150 amino acids in length for
most members. Solano, et al. suggest this protein acts
as a protease [Cell envelope, Biosynthesis and
degradation of surface polysaccharides and
lipopolysaccharides].
Length = 322
Score = 27.3 bits (61), Expect = 4.0
Identities = 7/15 (46%), Positives = 12/15 (80%)
Query: 5 IDDVAAAVNHLFDIP 19
++DV A+NH+F +P
Sbjct: 283 LNDVDIALNHIFKLP 297
>gnl|CDD|232956 TIGR00396, leuS_bact, leucyl-tRNA synthetase, eubacterial and
mitochondrial family. The leucyl-tRNA synthetases
belong to two families so broadly different that they
are represented by separate models. This model includes
both eubacterial and mitochondrial leucyl-tRNA
synthetases. It generates higher scores for some
valyl-tRNA synthetases than for any archaeal or
eukaryotic cytosolic leucyl-tRNA synthetase. Note that
the enzyme from Aquifex aeolicus is split into alpha and
beta chains; neither chain is long enough to score above
the trusted cutoff, but the alpha chain scores well
above the noise cutoff. The beta chain must be found by
a model and search designed for partial length matches
[Protein synthesis, tRNA aminoacylation].
Length = 842
Score = 27.0 bits (60), Expect = 4.8
Identities = 9/24 (37%), Positives = 14/24 (58%)
Query: 66 PKSDIQVTVEDERTLVIRSNGKRK 89
P D VED+ +V++ NGK +
Sbjct: 770 PVVDETALVEDKTLIVVQVNGKFR 793
>gnl|CDD|220931 pfam10995, DUF2819, Protein of unknown function (DUF2819). This
bacterial family of proteins has no known function.
Length = 316
Score = 26.8 bits (60), Expect = 5.6
Identities = 6/15 (40%), Positives = 12/15 (80%)
Query: 5 IDDVAAAVNHLFDIP 19
I+D+ A+N++F +P
Sbjct: 278 INDLDTALNNIFRLP 292
>gnl|CDD|215999 pfam00573, Ribosomal_L4, Ribosomal protein L4/L1 family. This
family includes Ribosomal L4/L1 from eukaryotes and
archaebacteria and L4 from eubacteria. L4 from yeast has
been shown to bind rRNA.
Length = 190
Score = 26.3 bits (59), Expect = 5.7
Identities = 15/53 (28%), Positives = 23/53 (43%), Gaps = 8/53 (15%)
Query: 102 RLERRVPQKLLRKFKLPEDANVSAISAKCENGVLTIVVEKLPPPPKPKTVEVA 154
++ +K+ R A SA+SAK G L +VV+ PKT +
Sbjct: 80 DYSYKLNKKVRRL------ALRSALSAKAREGKL-VVVDDF-ELEIPKTKDAV 124
>gnl|CDD|235221 PRK04123, PRK04123, ribulokinase; Provisional.
Length = 548
Score = 26.7 bits (60), Expect = 5.7
Identities = 8/20 (40%), Positives = 12/20 (60%)
Query: 120 DANVSAISAKCENGVLTIVV 139
DA++ A+ A E G L V+
Sbjct: 274 DAHMGAVGAGAEPGTLVKVM 293
>gnl|CDD|215518 PLN02959, PLN02959, aminoacyl-tRNA ligase.
Length = 1084
Score = 26.6 bits (59), Expect = 6.5
Identities = 16/43 (37%), Positives = 24/43 (55%), Gaps = 4/43 (9%)
Query: 36 TNKSKG-VSSIPVDILDSPKDYIFFMDVPGRPKSDIQVTVEDE 77
T+K G V+S+P D SP DY+ D+ +P + V+DE
Sbjct: 388 TDKGTGVVTSVPSD---SPDDYMALSDLKAKPALRAKYGVKDE 427
>gnl|CDD|222623 pfam14247, DUF4344, Domain of unknown function (DUF4344). This
family of proteins is found in bacteria and archaea.
Proteins in this family are typically between 247 and
291 amino acids in length. There is a conserved EED
sequence motif.
Length = 220
Score = 26.4 bits (59), Expect = 6.5
Identities = 8/22 (36%), Positives = 14/22 (63%)
Query: 2 SRVIDDVAAAVNHLFDIPETME 23
SRV++ +A +N LF +P +
Sbjct: 19 SRVLETLADLINRLFPLPYDLT 40
>gnl|CDD|215253 PLN02459, PLN02459, probable adenylate kinase.
Length = 261
Score = 26.3 bits (58), Expect = 6.6
Identities = 12/26 (46%), Positives = 16/26 (61%)
Query: 122 NVSAISAKCENGVLTIVVEKLPPPPK 147
NV+ I K E+G IV+ L PPP+
Sbjct: 164 NVADIDLKGEDGRPGIVMPPLLPPPE 189
>gnl|CDD|163567 TIGR03855, NAD_NadX, aspartate dehydrogenase. Members of this
protein family are L-aspartate dehydrogenase, as shown
for the NADP-dependent enzyme TM_1643 of Thermotoga
maritima. Members lack homology to NadB, the aspartate
oxidase (EC 1.4.3.16) of most mesophilic bacteria
(described by TIGR00551), which this enzyme replaces in
the generation of oxaloacetate from aspartate for the
NAD biosynthetic pathway. All members of the seed
alignment are found adjacent to other genes of NAD
biosynthesis, although other uses of L-aspartate
dehydrogenase may occur.
Length = 229
Score = 26.2 bits (58), Expect = 7.5
Identities = 12/35 (34%), Positives = 19/35 (54%)
Query: 120 DANVSAISAKCENGVLTIVVEKLPPPPKPKTVEVA 154
D N+ I + + G + I VE +P P P+T +A
Sbjct: 178 DRNIHEIFVESDFGEMEIRVENVPSPENPRTSYLA 212
>gnl|CDD|227434 COG5103, CDC39, Cell division control protein, negative regulator
of transcription [Cell division and chromosome
partitioning / Transcription].
Length = 2005
Score = 26.5 bits (58), Expect = 8.2
Identities = 15/57 (26%), Positives = 26/57 (45%), Gaps = 4/57 (7%)
Query: 92 DGEEEGCKCIRLERRVPQKLLRKFKL---PEDANVS-AISAKCENGVLTIVVEKLPP 144
+G + L R P+ +L+K +L + VS + E+ +L +V LPP
Sbjct: 418 NGAPNSFVFVVLFRTHPEMMLQKSRLVLAKDGIPVSRLLDIFLEHKMLPLVSNLLPP 474
>gnl|CDD|223569 COG0495, LeuS, Leucyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 814
Score = 26.5 bits (59), Expect = 8.8
Identities = 19/56 (33%), Positives = 27/56 (48%), Gaps = 5/56 (8%)
Query: 66 PKSDIQVTVEDERTLVIRSNGKRKRE-----DGEEEGCKCIRLERRVPQKLLRKFK 116
P+ D + VEDE +V++ NGK + D +EE K I L QK L+
Sbjct: 743 PEPDEEALVEDEVEIVVQVNGKVRAREVVAADADEEKVKEIALADEEVQKFLQGKT 798
>gnl|CDD|237343 PRK13304, PRK13304, L-aspartate dehydrogenase; Reviewed.
Length = 265
Score = 26.1 bits (58), Expect = 9.6
Identities = 13/31 (41%), Positives = 15/31 (48%)
Query: 120 DANVSAISAKCENGVLTIVVEKLPPPPKPKT 150
D NV I+ K G VE +P P PKT
Sbjct: 212 DRNVHEITVKGSFGTFKTRVENVPCPDNPKT 242
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
0.315 0.134 0.380
Gapped
Lambda K H
0.267 0.0709 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,106,943
Number of extensions: 732636
Number of successful extensions: 540
Number of sequences better than 10.0: 1
Number of HSP's gapped: 530
Number of HSP's successfully gapped: 45
Length of query: 156
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 67
Effective length of database: 6,990,096
Effective search space: 468336432
Effective search space used: 468336432
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: 42 (22.0 bits)
S2: 55 (25.0 bits)