RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2460
(83 letters)
>gnl|CDD|216043 pfam00651, BTB, BTB/POZ domain. The BTB (for BR-C, ttk and bab)
or POZ (for Pox virus and Zinc finger) domain is
present near the N-terminus of a fraction of zinc
finger (pfam00096) proteins and in proteins that
contain the pfam01344 motif such as Kelch and a family
of pox virus proteins. The BTB/POZ domain mediates
homomeric dimerisation and in some instances
heteromeric dimerisation. The structure of the
dimerised PLZF BTB/POZ domain has been solved and
consists of a tightly intertwined homodimer. The
central scaffolding of the protein is made up of a
cluster of alpha-helices flanked by short beta-sheets
at both the top and bottom of the molecule. POZ domains
from several zinc finger proteins have been shown to
mediate transcriptional repression and to interact with
components of histone deacetylase co-repressor
complexes including N-CoR and SMRT. The POZ or BTB
domain is also known as BR-C/Ttk or ZiN.
Length = 101
Score = 43.4 bits (103), Expect = 4e-07
Identities = 17/36 (47%), Positives = 19/36 (52%), Gaps = 2/36 (5%)
Query: 9 ELCDVTFLVGDTREPVCAVKAVLAARSRVFHKMLYS 44
ELCDVT +VGD KAVLAA S F +
Sbjct: 9 ELCDVTLVVGDKEFHAH--KAVLAACSPYFKALFTG 42
>gnl|CDD|197585 smart00225, BTB, Broad-Complex, Tramtrack and Bric a brac.
Domain in Broad-Complex, Tramtrack and Bric a brac.
Also known as POZ (poxvirus and zinc finger) domain.
Known to be a protein-protein interaction motif found
at the N-termini of several C2H2-type transcription
factors as well as Shaw-type potassium channels. Known
structure reveals a tightly intertwined dimer formed
via interactions between N-terminal strand and helix
structures. However in a subset of BTB/POZ domains,
these two secondary structures appear to be missing. Be
aware SMART predicts BTB/POZ domains without the beta1-
and alpha1-secondary structures.
Length = 97
Score = 37.7 bits (88), Expect = 6e-05
Identities = 23/85 (27%), Positives = 29/85 (34%), Gaps = 17/85 (20%)
Query: 12 DVTFLVGDTREPVCAVKAVLAARSRVFHKMLYSAPSPQRK-----KDPPPKENKLRLFLK 66
DVT +VG + KAVLAA S F + S K D P++ R L
Sbjct: 1 DVTLVVGGKKFHAH--KAVLAAHSPYFKALFSSDFKESDKSEIYLDDVSPED--FRALLN 56
Query: 67 --------RSSEPLLNLQNEAKLFQ 83
E + L A Q
Sbjct: 57 FLYTGKLDLPEENVEELLELADYLQ 81
>gnl|CDD|220180 pfam09325, Vps5, Vps5 C terminal like. Vps5 is a sorting nexin
that functions in membrane trafficking. This is the C
terminal dimerisation domain.
Length = 236
Score = 28.8 bits (65), Expect = 0.26
Identities = 11/53 (20%), Positives = 22/53 (41%), Gaps = 3/53 (5%)
Query: 26 AVKAVLAARSRVFHKMLYSAPSPQRKKDPPPKENKLRLFLKRSSEPLLNLQNE 78
+VKAV R + + + + +K+ + KL+ K + L + E
Sbjct: 122 SVKAVFNQRVKAWQQWQNAEQDLSKKRA---QLAKLKGAGKSRQDKLQQAKKE 171
>gnl|CDD|236252 PRK08376, PRK08376, putative monovalent cation/H+ antiporter
subunit D; Reviewed.
Length = 521
Score = 27.8 bits (62), Expect = 0.52
Identities = 13/41 (31%), Positives = 19/41 (46%), Gaps = 8/41 (19%)
Query: 23 PVCAVKAV------LAARSRVFHKMLYSAPSP--QRKKDPP 55
P+ V A+ LA+ +VFH + PS K+PP
Sbjct: 431 PILGVIAMIGSVLTLASFVKVFHTAFFGPPSEKVMNVKEPP 471
>gnl|CDD|225930 COG3395, COG3395, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 413
Score = 26.6 bits (59), Expect = 1.5
Identities = 9/28 (32%), Positives = 14/28 (50%)
Query: 26 AVKAVLAARSRVFHKMLYSAPSPQRKKD 53
AV VLA+ S ++Y++ P K
Sbjct: 291 AVAWVLASLSHGRAPLVYTSRGPDAIKA 318
>gnl|CDD|111933 pfam03092, BT1, BT1 family. Members of this family are
transmembrane proteins. Several are Leishmania putative
proteins that are thought to be pteridine transporters.
One such protein, previously termed (and is still
annotated as) ORFG, was shown to encode a biopterin
transport protein using null mutants, thus being
subsequently renamed BT1. The significant similarity of
ORFG/BT1 to Trypanosoma brucei ESAG10 (a putative
transmembrane protein and another member of this
family) was previously noted. This family also contains
five putative Arabidopsis thaliana proteins of unknown
function. In addition, it also contains two predicted
prokaryotic proteins (from the cyanobacteria
Synechocystis and Synechococcus).
Length = 425
Score = 25.0 bits (55), Expect = 6.0
Identities = 9/35 (25%), Positives = 13/35 (37%), Gaps = 2/35 (5%)
Query: 1 MKFLASMPELCDVTFLVGDTREPVCAVKAVLAARS 35
+K + L D L G R P A+ +L
Sbjct: 40 IKPFTGV--LSDGFALFGYRRRPYLALSGLLGGAF 72
>gnl|CDD|206747 cd01854, YjeQ_EngC, Ribosomal interacting GTPase YjeQ/EngC, a
circularly permuted subfamily of the Ras GTPases. YjeQ
(YloQ in Bacillus subtilis) is a ribosomal small
subunit-dependent GTPase; hence also known as RsgA. YjeQ
is a late-stage ribosomal biogenesis factor involved in
the 30S subunit maturation, and it represents a protein
family whose members are broadly conserved in bacteria
and have been shown to be essential to the growth of E.
coli and B. subtilis. Proteins of the YjeQ family
contain all sequence motifs typical of the vast class of
P-loop-containing GTPases, but show a circular
permutation, with a G4-G1-G3 pattern of motifs as
opposed to the regular G1-G3-G4 pattern seen in most
GTPases. All YjeQ family proteins display a unique
domain architecture, which includes an N-terminal
OB-fold RNA-binding domain, the central permuted GTPase
domain, and a zinc knuckle-like C-terminal cysteine
domain.
Length = 211
Score = 24.3 bits (54), Expect = 9.2
Identities = 11/29 (37%), Positives = 14/29 (48%), Gaps = 6/29 (20%)
Query: 20 TREPVCAVKAVLAA----RSRV--FHKML 42
EP CAVKA + A R + K+L
Sbjct: 182 INEPGCAVKAAVEAGEISEERYESYLKLL 210
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
0.321 0.134 0.390
Gapped
Lambda K H
0.267 0.0732 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,059,459
Number of extensions: 311455
Number of successful extensions: 282
Number of sequences better than 10.0: 1
Number of HSP's gapped: 280
Number of HSP's successfully gapped: 11
Length of query: 83
Length of database: 10,937,602
Length adjustment: 52
Effective length of query: 31
Effective length of database: 8,631,194
Effective search space: 267567014
Effective search space used: 267567014
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 (21.9 bits)
S2: 53 (24.2 bits)