RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8266
(68 letters)
>gnl|CDD|197674 smart00353, HLH, helix loop helix domain.
Length = 53
Score = 38.0 bits (89), Expect = 1e-05
Identities = 15/42 (35%), Positives = 24/42 (57%), Gaps = 1/42 (2%)
Query: 19 KRHRERLNAELDTLANLLPFEQNILSKLDRLSILRLSVSYLR 60
+R R ++N D L +LLP KL + ILRL++ Y++
Sbjct: 5 RRRRRKINEAFDELRSLLPTLPKN-KKLSKAEILRLAIEYIK 45
>gnl|CDD|238036 cd00083, HLH, Helix-loop-helix domain, found in specific DNA-
binding proteins that act as transcription factors;
60-100 amino acids long. A DNA-binding basic region is
followed by two alpha-helices separated by a variable
loop region; HLH forms homo- and heterodimers,
dimerization creates a parallel, left-handed, four
helix bundle; the basic region N-terminal to the first
amphipathic helix mediates high-affinity DNA-binding;
there are several groups of HLH proteins: those
(E12/E47) which bind specific hexanucleotide sequences
such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3),
those lacking the basic domain (Emc, Id) function as
negative regulators since they fail to bind DNA, those
(hairy, E(spl), deadpan) which repress transcription
although they can bind specific hexanucleotide
sequences such as N-box (5-CACGc/aG-3), those which
have a COE domain (Collier/Olf-1/EBF) which is involved
in both in dimerization and in DNA binding, and those
which bind pentanucleotides ACGTG or GCGTG and have a
PAS domain which allows the dimerization between PAS
proteins, the binding of small molecules (e.g.,
dioxin), and interactions with non-PAS proteins.
Length = 60
Score = 38.0 bits (89), Expect = 1e-05
Identities = 17/42 (40%), Positives = 24/42 (57%), Gaps = 1/42 (2%)
Query: 19 KRHRERLNAELDTLANLLPFEQNILSKLDRLSILRLSVSYLR 60
+R RER+N D L +LLP KL + ILR +V Y++
Sbjct: 13 RRRRERINDAFDELRSLLPTLPPS-KKLSKAEILRKAVDYIK 53
>gnl|CDD|215654 pfam00010, HLH, Helix-loop-helix DNA-binding domain.
Length = 52
Score = 33.2 bits (77), Expect = 8e-04
Identities = 16/42 (38%), Positives = 25/42 (59%), Gaps = 2/42 (4%)
Query: 19 KRHRERLNAELDTLANLLPFEQNILSKLDRLSILRLSVSYLR 60
+R R+R+N + L LLP N KL + ILRL++ Y++
Sbjct: 10 RRRRDRINDAFEELRELLPTPPN--KKLSKAEILRLAIEYIK 49
>gnl|CDD|232778 TIGR00006, TIGR00006, 16S rRNA
(cytosine(1402)-N(4))-methyltransferase. This model
describes RsmH, a 16S rRNA methyltransferase.
Previously, this gene was designated MraW, known to be
essential in E. coli and widely conserved in bacteria
[Cell envelope, Biosynthesis and degradation of murein
sacculus and peptidoglycan].
Length = 307
Score = 28.1 bits (63), Expect = 0.23
Identities = 18/55 (32%), Positives = 25/55 (45%), Gaps = 4/55 (7%)
Query: 2 ISLKPPPKDGVTKSNPSKRH----RERLNAELDTLANLLPFEQNILSKLDRLSIL 52
IS P +P+ R R +N EL+ L L F N+L+ RLSI+
Sbjct: 183 ISKAVPGFSKYKSIHPATRVFQAIRIYVNDELEELEEALQFAPNLLAPGGRLSII 237
>gnl|CDD|224420 COG1503, eRF1, Peptide chain release factor 1 (eRF1)
[Translation, ribosomal structure and biogenesis].
Length = 411
Score = 26.9 bits (60), Expect = 0.60
Identities = 12/53 (22%), Positives = 22/53 (41%), Gaps = 13/53 (24%)
Query: 1 MISLKPPPKDGVTKSNPSKRHRERLNAELDTLANLLPFEQNILSKLDRLSILR 53
+ISL PP +++ ++ L + NI SK+ R ++L
Sbjct: 29 LISLYIPPD-------------RQISDVVNRLRDEYSTASNIKSKVTRKNVLS 68
>gnl|CDD|205992 pfam13821, DUF4187, Domain of unknown function (DUF4187). This
family is found at the very C-terminus of proteins that
carry a G-patch domain, pfam01585. The domain is short
and cysteine-rich.
Length = 55
Score = 25.7 bits (57), Expect = 0.66
Identities = 10/27 (37%), Positives = 15/27 (55%), Gaps = 3/27 (11%)
Query: 39 EQNILSKLDRLSILRLSVSYLRTKSYF 65
E LS +RL +L +SYLR + +
Sbjct: 6 EFEELSPEERLQLL---LSYLREEHNY 29
>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 = 26.5 bits (59), Expect = 1.1
Identities = 11/60 (18%), Positives = 27/60 (45%), Gaps = 4/60 (6%)
Query: 12 VTKSNPSKRHRERLNAELDTLANLLPFEQNILSKLDR----LSILRLSVSYLRTKSYFQE 67
+T P++ + L+ E A + ++ L R ++ L ++ L+++S F +
Sbjct: 92 LTGEVPTEEQVDELSKEWAKRAEVPSHVVKMIDNLPRNLHPMTQLSAAILALQSESKFAK 151
>gnl|CDD|216253 pfam01029, NusB, NusB family. The NusB protein is involved in
the regulation of rRNA biosynthesis by transcriptional
antitermination.
Length = 126
Score = 25.6 bits (57), Expect = 1.8
Identities = 14/37 (37%), Positives = 22/37 (59%), Gaps = 3/37 (8%)
Query: 20 RHRERLNAELDTLANLLPFEQNILSKLDRLSILRLSV 56
R+ E L+A ++ L P E+ L +DR +ILRL +
Sbjct: 50 RNLEELDALIEKLLENWPLER--LDPVDR-AILRLGL 83
>gnl|CDD|233518 TIGR01665, put_anti_recept, phage minor structural protein,
N-terminal region. This model represents the conserved
N-terminal region, typically from about residue 25 to
about residue 350, of a family of uncharacterized phage
proteins 500 to 1700 residues in length [Mobile and
extrachromosomal element functions, Prophage
functions].
Length = 316
Score = 25.4 bits (56), Expect = 2.1
Identities = 10/47 (21%), Positives = 18/47 (38%)
Query: 19 KRHRERLNAELDTLANLLPFEQNILSKLDRLSILRLSVSYLRTKSYF 65
LDTL LPF+ + K+ + ++ L+ + F
Sbjct: 2 DIKISEEKNNLDTLTFSLPFDDPLWEKIKEENYIKKHDDDLKNEQLF 48
>gnl|CDD|226828 COG4393, COG4393, Predicted membrane protein [Function unknown].
Length = 405
Score = 25.2 bits (55), Expect = 2.8
Identities = 13/44 (29%), Positives = 17/44 (38%)
Query: 16 NPSKRHRERLNAELDTLANLLPFEQNILSKLDRLSILRLSVSYL 59
K L A L L PF + L RL L+L+ S +
Sbjct: 145 FQLKSSLAPLLALLIYLILSFPFSARGVLALMRLRFLKLTKSLV 188
>gnl|CDD|223352 COG0275, COG0275, Predicted S-adenosylmethionine-dependent
methyltransferase involved in cell envelope biogenesis
[Cell envelope biogenesis, outer membrane].
Length = 314
Score = 24.9 bits (55), Expect = 4.1
Identities = 14/49 (28%), Positives = 23/49 (46%), Gaps = 4/49 (8%)
Query: 7 PPKDGVTKSNPSKRH----RERLNAELDTLANLLPFEQNILSKLDRLSI 51
P K+ K +P+ R R +N EL+ L L ++L RL++
Sbjct: 194 PAKEKRKKIHPATRTFQAIRIYVNDELEELEEALEAALDLLKPGGRLAV 242
>gnl|CDD|236279 PRK08508, PRK08508, biotin synthase; Provisional.
Length = 279
Score = 24.6 bits (54), Expect = 4.4
Identities = 9/24 (37%), Positives = 13/24 (54%)
Query: 36 LPFEQNILSKLDRLSILRLSVSYL 59
LP + LS + L I+RL+ L
Sbjct: 194 LPLKAPTLSADEALEIVRLAKEAL 217
>gnl|CDD|188032 TIGR00195, exoDNase_III, exodeoxyribonuclease III. The model
brings in reverse transcriptases at scores below 50,
model also contains eukaryotic apurinic/apyrimidinic
endonucleases which group in the same family [DNA
metabolism, DNA replication, recombination, and repair].
Length = 254
Score = 24.3 bits (53), Expect = 5.8
Identities = 12/33 (36%), Positives = 15/33 (45%), Gaps = 4/33 (12%)
Query: 16 NPSKRHRERLNAELDTLANLLPFEQNILSKLDR 48
N S+ E+L +L L L QN L KL
Sbjct: 108 NGSRDDSEKLPYKLQWLEAL----QNYLEKLVD 136
>gnl|CDD|220491 pfam09958, DUF2192, Uncharacterized protein conserved in archaea
(DUF2192). This domain, found in various hypothetical
archaeal proteins, has no known function.
Length = 231
Score = 23.8 bits (52), Expect = 7.9
Identities = 12/33 (36%), Positives = 20/33 (60%), Gaps = 2/33 (6%)
Query: 21 HRERLNAELDTLANLLPFEQNILSKLDRLSILR 53
+RER+ D L+ LL E IL++ D + +L+
Sbjct: 6 YRERIEVLTDLLSRLL--EGEILTREDLIELLQ 36
>gnl|CDD|233256 TIGR01063, gyrA, DNA gyrase, A subunit. This model describes the
common type II DNA topoisomerase (DNA gyrase). Two
apparently independently arising families, one in the
Proteobacteria and one in Gram-positive lineages, are
both designated toposisomerase IV [DNA metabolism, DNA
replication, recombination, and repair].
Length = 800
Score = 23.8 bits (52), Expect = 9.8
Identities = 9/28 (32%), Positives = 16/28 (57%)
Query: 22 RERLNAELDTLANLLPFEQNILSKLDRL 49
RE+L E L L+ ++IL+ +R+
Sbjct: 429 REKLQEEYKELLELIADLEDILASEERV 456
>gnl|CDD|206130 pfam13960, DUF4218, Domain of unknown function (DUF4218).
Length = 129
Score = 23.3 bits (51), Expect = 9.8
Identities = 10/17 (58%), Positives = 10/17 (58%)
Query: 9 KDGVTKSNPSKRHRERL 25
DGVT NP RH RL
Sbjct: 113 SDGVTIGNPVPRHEGRL 129
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 0.133 0.362
Gapped
Lambda K H
0.267 0.0777 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,317,510
Number of extensions: 235109
Number of successful extensions: 286
Number of sequences better than 10.0: 1
Number of HSP's gapped: 282
Number of HSP's successfully gapped: 23
Length of query: 68
Length of database: 10,937,602
Length adjustment: 39
Effective length of query: 29
Effective length of database: 9,207,796
Effective search space: 267026084
Effective search space used: 267026084
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 (24.1 bits)