RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17316
(229 letters)
>gnl|CDD|203213 pfam05225, HTH_psq, helix-turn-helix, Psq domain. This
DNA-binding motif is found in four copies in the
pipsqueak protein of Drosophila melanogaster. In
pipsqueak this domain binds to GAGA sequence.
Length = 43
Score = 53.3 bits (129), Expect = 3e-10
Identities = 22/44 (50%), Positives = 28/44 (63%), Gaps = 1/44 (2%)
Query: 36 EDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGIHTPK 79
ED+ ALEA+R G+MSL KA+ YGIP +TLW R R +
Sbjct: 1 EDLAEALEAVRNGKMSLRKAARKYGIPRSTLW-RRLRGKYSLKR 43
Score = 46.0 bits (110), Expect = 2e-07
Identities = 19/40 (47%), Positives = 26/40 (65%), Gaps = 2/40 (5%)
Query: 122 EILNVALDALRAGSISANKASKAYGIPSSTLYKIARKEGI 161
E L AL+A+R G +S KA++ YGIP STL++ R G
Sbjct: 1 EDLAEALEAVRNGKMSLRKAARKYGIPRSTLWR--RLRGK 38
Score = 46.0 bits (110), Expect = 2e-07
Identities = 18/43 (41%), Positives = 29/43 (67%)
Query: 177 EDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCKLSRSTPR 219
EDL ALE +R+G+ ++++A+ +YGIP TL+ R + S R
Sbjct: 1 EDLAEALEAVRNGKMSLRKAARKYGIPRSTLWRRLRGKYSLKR 43
Score = 30.2 bits (69), Expect = 0.081
Identities = 12/25 (48%), Positives = 17/25 (68%)
Query: 90 EILNVALDALRAGSISANKASKAYG 114
E L AL+A+R G +S KA++ YG
Sbjct: 1 EDLAEALEAVRNGKMSLRKAARKYG 25
>gnl|CDD|225440 COG2886, COG2886, Uncharacterized small protein [Function unknown].
Length = 88
Score = 30.8 bits (70), Expect = 0.13
Identities = 12/44 (27%), Positives = 25/44 (56%)
Query: 120 NEEILNVALDALRAGSISANKASKAYGIPSSTLYKIARKEGIRL 163
+E L +A++ + G++S +A++ G+ + + RK GI L
Sbjct: 26 SELRLEIAIELFQEGAVSLGRAAELAGMSLNEFEEELRKRGIPL 69
>gnl|CDD|225822 COG3284, AcoR, Transcriptional activator of acetoin/glycerol
metabolism [Secondary metabolites biosynthesis,
transport, and catabolism / Transcription].
Length = 606
Score = 31.6 bits (72), Expect = 0.33
Identities = 13/37 (35%), Positives = 23/37 (62%)
Query: 39 DAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGI 75
A L AL+A ++++A+ GI +TL+++ R GI
Sbjct: 568 AALLAALQATNGNISEAARLLGISRSTLYRKLKRHGI 604
Score = 30.4 bits (69), Expect = 0.86
Identities = 16/37 (43%), Positives = 23/37 (62%), Gaps = 4/37 (10%)
Query: 128 LDALRA--GSISANKASKAYGIPSSTLYKIARKEGIR 162
L AL+A G+IS A++ GI STLY+ ++ GI
Sbjct: 571 LAALQATNGNISE--AARLLGISRSTLYRKLKRHGIS 605
>gnl|CDD|226350 COG3829, RocR, Transcriptional regulator containing PAS, AAA-type
ATPase, and DNA-binding domains [Transcription / Signal
transduction mechanisms].
Length = 560
Score = 29.2 bits (66), Expect = 1.8
Identities = 15/77 (19%), Positives = 28/77 (36%), Gaps = 2/77 (2%)
Query: 1 MMITPELLGLLPSSNYSDGETDKAGSLTVTKTWTHEDMDAAL--EALRAGQMSLTKASVS 58
+I + L + E+ + L EAL + +KA+
Sbjct: 483 GLIDADDLPAFALEEKEPRPETTKQIEVGSLKEALEEYEKHLIREALERHGGNKSKAAKE 542
Query: 59 YGIPSTTLWQRAHRLGI 75
GI TTL+++ + G+
Sbjct: 543 LGISRTTLYRKLKKYGL 559
Score = 28.0 bits (63), Expect = 5.2
Identities = 13/35 (37%), Positives = 21/35 (60%)
Query: 128 LDALRAGSISANKASKAYGIPSSTLYKIARKEGIR 162
+AL + +KA+K GI +TLY+ +K G+R
Sbjct: 526 REALERHGGNKSKAAKELGISRTTLYRKLKKYGLR 560
>gnl|CDD|224872 COG1961, PinR, Site-specific recombinases, DNA invertase Pin
homologs [DNA replication, recombination, and repair].
Length = 222
Score = 28.2 bits (63), Expect = 2.7
Identities = 14/43 (32%), Positives = 20/43 (46%)
Query: 120 NEEILNVALDALRAGSISANKASKAYGIPSSTLYKIARKEGIR 162
EE L G S ++ ++A GI ST+Y+I K R
Sbjct: 162 AEEQAAAVRRLLADGLGSYSEIARALGISRSTVYRILNKLKKR 204
>gnl|CDD|189996 pfam01464, SLT, Transglycosylase SLT domain. This family is
distantly related to pfam00062. Members are found in
phages, type II, type III and type IV secretion systems.
Length = 117
Score = 27.3 bits (61), Expect = 3.1
Identities = 10/21 (47%), Positives = 14/21 (66%)
Query: 139 NKASKAYGIPSSTLYKIARKE 159
KA++ YGI S L IA++E
Sbjct: 4 IKAAEKYGIDPSLLAAIAQQE 24
>gnl|CDD|233949 TIGR02607, antidote_HigA, addiction module antidote protein, HigA
family. Members of this family form a distinct clade
within the larger family HTH_3 of helix-turn-helix
proteins, described by pfam01381. Members of this clade
are strictly bacterial and nearly always shorter than
110 amino acids. This family includes the characterized
member HigA, without which the killer protein HigB
cannot be cloned. The hig (host inhibition of growth)
system is noted to be unusual in that killer protein is
uncoded by the upstream member of the gene pair
[Regulatory functions, DNA interactions, Regulatory
functions, Protein interactions, Mobile and
extrachromosomal element functions, Other].
Length = 78
Score = 26.8 bits (60), Expect = 3.1
Identities = 18/60 (30%), Positives = 25/60 (41%), Gaps = 9/60 (15%)
Query: 122 EILNVALDALRAGSISANKASKAYGIPSSTLYKIARKEG-------IRLAQPFNASPTAW 174
EIL + L +S +KA G+ STL +I +RLA+ SP W
Sbjct: 7 EILRE--EFLEPLGLSIRALAKALGVSRSTLSRIVNGRRGITADMALRLAKALGTSPEFW 64
>gnl|CDD|225114 COG2204, AtoC, Response regulator containing CheY-like receiver,
AAA-type ATPase, and DNA-binding domains [Signal
transduction mechanisms].
Length = 464
Score = 28.4 bits (64), Expect = 3.8
Identities = 18/86 (20%), Positives = 31/86 (36%), Gaps = 5/86 (5%)
Query: 3 ITPELLGLLPSSNYSDGETDKAGSLTVTKTWTHEDMDAA-----LEALRAGQMSLTKASV 57
I E L L + ++ AG + E + L+AL + ++A+
Sbjct: 379 IEVEDLPLEILAPAAEALAGPAGEAALPGLPLGEALAEVERQLILQALERTGGNKSEAAE 438
Query: 58 SYGIPSTTLWQRAHRLGIHTPKKEGP 83
GI TL+++ GI E
Sbjct: 439 RLGISRKTLYRKLKEYGIDRSDVERS 464
>gnl|CDD|146404 pfam03746, LamB_YcsF, LamB/YcsF family. This family includes LamB.
The lam locus of Aspergillus nidulans consists of two
divergently transcribed genes, lamA and lamB, involved
in the utilisation of lactams such as 2-pyrrolidinone.
Both genes are under the control of the positive
regulatory gene amdR and are subject to carbon and
nitrogen metabolite repression. The exact molecular
function of the proteins in this family is unknown.
Length = 242
Score = 27.3 bits (61), Expect = 6.1
Identities = 10/46 (21%), Positives = 19/46 (41%), Gaps = 4/46 (8%)
Query: 120 NEEILNVALDALRAGSISANKASKAYGIPSSTLYKIARKEGIRLAQ 165
+ + +A+ + A G+ S L A++ G+RLA
Sbjct: 120 DRALARAVAEAVYD----FDPALPLMGLAGSALLDAAKEAGLRLAF 161
>gnl|CDD|145774 pfam02796, HTH_7, Helix-turn-helix domain of resolvase.
Length = 45
Score = 25.0 bits (55), Expect = 7.4
Identities = 14/46 (30%), Positives = 21/46 (45%), Gaps = 1/46 (2%)
Query: 114 GPTKSWNEEILNVALDALRAGSISANKASKAYGIPSSTLYKIARKE 159
G NEE +N + L IS + +K +GI ST+Y+
Sbjct: 1 GRPPKLNEEDINEVI-TLLEEGISIKQIAKIFGISRSTVYRYLAAS 45
>gnl|CDD|176240 cd08279, Zn_ADH_class_III, Class III alcohol dehydrogenase.
Glutathione-dependent formaldehyde dehydrogenases (FDHs,
Class III ADH) are members of the zinc-dependent/medium
chain alcohol dehydrogenase family. FDH converts
formaldehyde and NAD(P) to formate and NAD(P)H. The
initial step in this process the spontaneous formation
of a S-(hydroxymethyl)glutathione adduct from
formaldehyde and glutathione, followed by FDH-mediated
oxidation (and detoxification) of the adduct to
S-formylglutathione. NAD(P)(H)-dependent oxidoreductases
are the major enzymes in the interconversion of alcohols
and aldehydes or ketones. 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. Class III ADH are also known as
glutathione-dependent formaldehyde dehydrogenase (FDH),
which convert aldehydes to corresponding carboxylic acid
and alcohol. ADH is a member of the medium chain
alcohol dehydrogenase family (MDR), which has a
NAD(P)(H)-binding domain in a Rossmann fold of an
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.
Length = 363
Score = 27.1 bits (61), Expect = 7.5
Identities = 13/45 (28%), Positives = 22/45 (48%), Gaps = 7/45 (15%)
Query: 5 PELLGLLPSSNYSDGETDKAGSLTVTKTWTHEDMDAALEALRAGQ 49
P LL L Y G K L VT+ ++ ++++ A + AG+
Sbjct: 319 PRLLDL-----YRAGRL-KLDEL-VTRRYSLDEINEAFADMLAGE 356
>gnl|CDD|181292 PRK08208, PRK08208, coproporphyrinogen III oxidase; Validated.
Length = 430
Score = 27.3 bits (61), Expect = 8.2
Identities = 11/32 (34%), Positives = 15/32 (46%)
Query: 34 THEDMDAALEALRAGQMSLTKASVSYGIPSTT 65
D+ ALE +RA + + YGIP T
Sbjct: 175 KRADVHQALEWIRAAGFPILNIDLIYGIPGQT 206
>gnl|CDD|240852 cd12406, RRM4_NCL, RNA recognition motif 4 in vertebrate nucleolin.
This subfamily corresponds to the RRM4 of ubiquitously
expressed protein nucleolin, also termed protein C23, is
a multifunctional major nucleolar phosphoprotein that
has been implicated in various metabolic processes, such
as ribosome biogenesis, cytokinesis, nucleogenesis, cell
proliferation and growth, cytoplasmic-nucleolar
transport of ribosomal components, transcriptional
repression, replication, signal transduction, inducing
chromatin decondensation, etc. Nucleolin exhibits
intrinsic self-cleaving, DNA helicase, RNA helicase and
DNA-dependent ATPase activities. It can be
phosphorylated by many protein kinases, such as the
major mitotic kinase Cdc2, casein kinase 2 (CK2), and
protein kinase C-zeta. Nucleolin shares similar domain
architecture with gar2 from Schizosaccharomyces pombe
and NSR1 from Saccharomyces cerevisiae. The highly
phosphorylated N-terminal domain of nucleolin is made up
of highly acidic regions separated from each other by
basic sequences, and contains multiple phosphorylation
sites. The central domain of nucleolin contains four
closely adjacent N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), which suggests that
nucleolin is potentially able to interact with multiple
RNA targets. The C-terminal RGG (or GAR) domain of
nucleolin is rich in glycine, arginine and phenylalanine
residues, and contains high levels of
NG,NG-dimethylarginines. .
Length = 78
Score = 25.7 bits (56), Expect = 8.6
Identities = 19/71 (26%), Positives = 32/71 (45%), Gaps = 3/71 (4%)
Query: 81 EGPTKSWNEEILNVALDALRAGSISANK---ASKAYGPTKSWNEEILNVALDALRAGSIS 137
+G ++ EE L + D A I ++ +SK +G +EE A +A+ G I
Sbjct: 6 KGLSEDTTEETLKESFDGSIAARIVTDRDTGSSKGFGFVDFSSEEDAKAAKEAMEDGEID 65
Query: 138 ANKASKAYGIP 148
NK + + P
Sbjct: 66 GNKVTLDFAKP 76
>gnl|CDD|233715 TIGR02086, IPMI_arch, 3-isopropylmalate dehydratase, large subunit.
This subfamily is a subset of the larger HacA family
(Homoaconitate hydratase family, TIGR01343) and is most
closely related to the 3-isopropylmalate dehydratase,
large subunits which form TIGR00170. This subfamily
includes the members of TIGR01343 which are gene
clustered with other genes of leucine biosynthesis. The
rest of the subfamily includes mainly archaeal species
which exhibit two hits to this model. In these cases it
is possible that one or the other of the hits does not
have a 3-isopropylmalate dehydratase activity but rather
one of the other related aconitase-like activities.
Length = 412
Score = 27.0 bits (60), Expect = 8.9
Identities = 12/35 (34%), Positives = 17/35 (48%)
Query: 153 YKIARKEGIRLAQPFNASPTAWKPEDLEIALEGIR 187
++ EG + Q F S T + EDL IA E +
Sbjct: 276 RPVSDVEGTEIDQVFIGSCTNGRIEDLRIAAEILE 310
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
0.310 0.126 0.365
Gapped
Lambda K H
0.267 0.0833 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,487,201
Number of extensions: 1038417
Number of successful extensions: 966
Number of sequences better than 10.0: 1
Number of HSP's gapped: 965
Number of HSP's successfully gapped: 25
Length of query: 229
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 135
Effective length of database: 6,768,326
Effective search space: 913724010
Effective search space used: 913724010
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: 57 (25.5 bits)