RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8988
(133 letters)
>gnl|CDD|215654 pfam00010, HLH, Helix-loop-helix DNA-binding domain.
Length = 52
Score = 67.5 bits (166), Expect = 2e-16
Identities = 26/52 (50%), Positives = 36/52 (69%), Gaps = 1/52 (1%)
Query: 43 QRRAANIRERRRMFNLNEAFDKLRRKVPTFAYEKRLSRIETLRLAITYISFM 94
+R+A N RERRR +N+AF++LR +PT K+LS+ E LRLAI YI +
Sbjct: 1 RRKAHNERERRRRDRINDAFEELRELLPT-PPNKKLSKAEILRLAIEYIKHL 51
>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 = 67.6 bits (166), Expect = 2e-16
Identities = 28/57 (49%), Positives = 38/57 (66%)
Query: 43 QRRAANIRERRRMFNLNEAFDKLRRKVPTFAYEKRLSRIETLRLAITYISFMSELLH 99
+R A N+RERRR +N+AFD+LR +PT K+LS+ E LR A+ YI + ELL
Sbjct: 4 RREAHNLRERRRRERINDAFDELRSLLPTLPPSKKLSKAEILRKAVDYIKSLQELLQ 60
>gnl|CDD|197674 smart00353, HLH, helix loop helix domain.
Length = 53
Score = 64.9 bits (159), Expect = 2e-15
Identities = 28/52 (53%), Positives = 34/52 (65%)
Query: 48 NIRERRRMFNLNEAFDKLRRKVPTFAYEKRLSRIETLRLAITYISFMSELLH 99
N RERRR +NEAFD+LR +PT K+LS+ E LRLAI YI + E L
Sbjct: 1 NARERRRRRKINEAFDELRSLLPTLPKNKKLSKAEILRLAIEYIKSLQEELQ 52
>gnl|CDD|227070 COG4726, PilX, Tfp pilus assembly protein PilX [Cell motility and
secretion / Intracellular trafficking and secretion].
Length = 196
Score = 28.3 bits (63), Expect = 0.91
Identities = 10/25 (40%), Positives = 13/25 (52%)
Query: 37 RVATLAQRRAANIRERRRMFNLNEA 61
R L +R +AN R+R F EA
Sbjct: 36 RSVLLQERISANERDRSLAFQAAEA 60
>gnl|CDD|221752 pfam12752, SUZ, SUZ domain. The SUZ domain is a conserved
RNA-binding domain found in eukaryotes and enriched in
positively charged amino acids. It was first
characterized in the C.elegans protein Szy-20 where it
has been shown to bind RNA and allow their localization
to the centrosome. Warning- the domain has a
compositionally biased character.
Length = 57
Score = 25.8 bits (57), Expect = 2.1
Identities = 10/38 (26%), Positives = 17/38 (44%)
Query: 20 GGSSTGTNGGHTKKTRRRVATLAQRRAANIRERRRMFN 57
S+G++ G R+ +L +R A R R+F
Sbjct: 17 ESGSSGSSPGDKGAKDRKAKSLEEREAEYAEARERIFG 54
>gnl|CDD|182514 PRK10520, rhtB, homoserine/homoserine lactone efflux protein;
Provisional.
Length = 205
Score = 26.6 bits (59), Expect = 3.4
Identities = 13/27 (48%), Positives = 17/27 (62%)
Query: 39 ATLAQRRAANIRERRRMFNLNEAFDKL 65
ATLAQR A I+ ++M LN+ F L
Sbjct: 166 ATLAQRIARWIKGPKQMKALNKIFGSL 192
>gnl|CDD|217627 pfam03585, Herpes_ICP4_C, Herpesvirus ICP4-like protein C-terminal
region. The immediate-early protein ICP4 (infected-cell
polypeptide 4) is required for efficient transcription
of early and late viral genes and is thus essential for
productive infection. ICP4 is a large phosphoprotein
that binds DNA in a sequence specific manner as a
homodimer. ICP4 represses transcription from LAT, ICP4
and ORF-P that have high-affinity a ICP4 binding site
that spans the transcription initiation site. ICP4
proteins have two highly conserved regions, this family
contains the C-terminal region that probably acts as an
enhancer for the N-terminal region.
Length = 425
Score = 27.0 bits (60), Expect = 3.6
Identities = 19/74 (25%), Positives = 30/74 (40%), Gaps = 4/74 (5%)
Query: 38 VATLAQRRAANIRERRRMFNLNEAFDKLRRKVPTFAYEKRLSRIETLRLAITYISFMSE- 96
+A +A R R F A LRR+ A+ ++++ E +R+ + Y E
Sbjct: 54 LAEIAARCNGPPPRSDRGFGPLTASGPLRRRT---AWMRQIADPEDVRVVVLYSPLPGEH 110
Query: 97 LLHGTPNGSTSGSP 110
L P G G P
Sbjct: 111 LFGVPPPGDPPGGP 124
>gnl|CDD|221293 pfam11890, DUF3410, Domain of unknown function (DUF3410). This
domain is functionally uncharacterized. This domain is
found in bacteria. This presumed domain is about 90
amino acids in length. This domain is found associated
with pfam02826, pfam00389. This domain has a conserved
RRE sequence motif.
Length = 81
Score = 25.3 bits (56), Expect = 4.7
Identities = 6/15 (40%), Positives = 7/15 (46%)
Query: 53 RRMFNLNEAFDKLRR 67
RR FD LR+
Sbjct: 39 RRNLERPGGFDYLRK 53
>gnl|CDD|223039 PHA03307, PHA03307, transcriptional regulator ICP4; Provisional.
Length = 1352
Score = 26.7 bits (59), Expect = 5.1
Identities = 16/74 (21%), Positives = 28/74 (37%), Gaps = 4/74 (5%)
Query: 38 VATLAQRRAANIRERRRMFNLNEAFDKLRRKVPTFAYEKRLSRIETLRLAITYISFMSE- 96
+A +A R F A LRR+ A+ +++ E +R+ + Y E
Sbjct: 978 LAEIAARCGGPPPRSGSAFGPLRASGPLRRRA---AWMRQIPDPEDVRVVVLYSPLPGEH 1034
Query: 97 LLHGTPNGSTSGSP 110
L ++ G P
Sbjct: 1035 LFGVPAPDASPGGP 1048
>gnl|CDD|233148 TIGR00844, c_cpa1, na(+)/h(+) antiporter. The Monovalent
Cation:Proton Antiporter-1 (CPA1) Family (TC 2.A.36) The
CPA1 family is a large family of proteins derived from
Gram-positive and Gram-negative bacteria, blue green
bacteria, yeast, plants and animals. Transporters from
eukaryotes have been functionally characterized, and all
of these catalyze Na+:H+ exchange. Their primary
physiological functions may be in (1) cytoplasmic pH
regulation, extruding the H+ generated during
metabolism, and (2) salt tolerance (in plants), due to
Na+ uptake into vacuoles. This model is specific for the
fungal members of this family [Transport and binding
proteins, Cations and iron carrying compounds].
Length = 810
Score = 26.4 bits (58), Expect = 5.3
Identities = 25/126 (19%), Positives = 40/126 (31%), Gaps = 13/126 (10%)
Query: 8 LECLFNGRLSGHGGSSTGTNGGHTKKTRRRVAT------LAQRRAANIRERRRMFNLNEA 61
+ L RL + T T T + L +R NI+ER N
Sbjct: 528 MNDLGRERLQKEKEAHAATFDLSTTTTTQLGTENGRGGGLEERSKTNIKERSENVNTIYG 587
Query: 62 FDKLRRKVPTFAYEKRLSRIETLRLAITYISFMSELLHGTPNGSTSGSP---IYQMSQRE 118
DKL R + ++ + T R + + S + S I ++ + E
Sbjct: 588 LDKLARDTEN----RDVTYVPTSRYDGIESEIDDVYTYENDSESIASSERRRIKKLREEE 643
Query: 119 YIPYTA 124
Y A
Sbjct: 644 QQAYIA 649
>gnl|CDD|215531 PLN02981, PLN02981, glucosamine:fructose-6-phosphate
aminotransferase.
Length = 680
Score = 26.3 bits (58), Expect = 6.0
Identities = 12/25 (48%), Positives = 14/25 (56%), Gaps = 2/25 (8%)
Query: 3 KSKAILECLFNG--RLSGHGGSSTG 25
+ + ILE LFNG RL G S G
Sbjct: 15 ERRFILEVLFNGLRRLEYRGYDSAG 39
>gnl|CDD|234281 TIGR03619, F420_Rv2161c, probable F420-dependent oxidoreductase,
Rv2161c family. Coenzyme F420 has a limited
phylogenetic distribution, including methanogenic
archaea, Mycobacterium tuberculosis and related species,
Colwellia psychrerythraea 34H, Rhodopseudomonas
palustris HaA2, and others. Partial phylogenetic
profiling identifies protein subfamilies, within the
larger family called luciferase-like monooxygenanases
(pfam00296), that appear only in F420-positive genomes
and are likely to be F420-dependent. This model
describes a domain found in a distinctive subset of
bacterial luciferase homologs, found only in
F420-biosynthesizing members of the Actinobacteria
[Unknown function, Enzymes of unknown specificity].
Length = 246
Score = 26.1 bits (58), Expect = 6.7
Identities = 8/59 (13%), Positives = 14/59 (23%), Gaps = 8/59 (13%)
Query: 28 GGHTKKTRRRVATLAQ------RRAANIRERRRMFNLNEAFDKLRRKVPTFAYEKRLSR 80
GG+++ RR A L + L + R +
Sbjct: 163 GGNSEAALRRAARLGDGWMPFGPPVDRLAAAVAR--LRDLAAAAGRDPDAVEVVLVRTD 219
>gnl|CDD|225426 COG2871, NqrF, Na+-transporting NADH:ubiquinone oxidoreductase,
subunit NqrF [Energy production and conversion].
Length = 410
Score = 25.9 bits (57), Expect = 6.8
Identities = 12/30 (40%), Positives = 16/30 (53%), Gaps = 1/30 (3%)
Query: 50 RERRRMFNLNEAFDKLRRKVPTFAYEKRLS 79
R R MF E FD+L+ + P F + LS
Sbjct: 314 RSLREMF-YQEDFDQLQAENPNFHWHLALS 342
>gnl|CDD|218816 pfam05936, DUF876, Bacterial protein of unknown function (DUF876).
This family consists of a series of hypothetical
bacterial sequences of unknown function.
Length = 427
Score = 26.0 bits (58), Expect = 7.5
Identities = 18/73 (24%), Positives = 27/73 (36%), Gaps = 10/73 (13%)
Query: 36 RRVATLAQRRAANIRERRR-----MFNLNEAFDKLR-----RKVPTFAYEKRLSRIETLR 85
R + L + RA + R R F + + D L R P A+ RL ++ R
Sbjct: 186 RELLGLLRARAEALAGRLRGSSQQKFGVADVSDFLLLQALNRAEPLLAHLLRLPQLHPER 245
Query: 86 LAITYISFMSELL 98
L + EL
Sbjct: 246 LYRELLRLAGELS 258
>gnl|CDD|131576 TIGR02524, dot_icm_DotB, Dot/Icm secretion system ATPase DotB.
Members of this protein family are the DotB component of
Dot/Icm secretion systems, as found in obligate
intracellular pathogens Legionella pneumophila and
Coxiella burnetii. While this system resembles type IV
secretion systems and has been called a form of type IV,
the liturature now seems to favor calling this the
Dot/Icm system. This family is most closely related to
TraJ proteins of plasmid transfer, rather than to
proteins of other type IV secretion systems.
Length = 358
Score = 25.7 bits (56), Expect = 8.6
Identities = 13/30 (43%), Positives = 19/30 (63%), Gaps = 4/30 (13%)
Query: 63 DKLRRKVPTFAYEKRLSR----IETLRLAI 88
+ +RR V +F E+R+ R IET+RL I
Sbjct: 251 ETIRRLVGSFPAEERIGRTIDIIETIRLCI 280
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
0.319 0.133 0.380
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: 6,896,119
Number of extensions: 617127
Number of successful extensions: 660
Number of sequences better than 10.0: 1
Number of HSP's gapped: 658
Number of HSP's successfully gapped: 29
Length of query: 133
Length of database: 10,937,602
Length adjustment: 86
Effective length of query: 47
Effective length of database: 7,123,158
Effective search space: 334788426
Effective search space used: 334788426
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 53 (24.1 bits)